From 636e3f0c9415db6505fba29a45aa98cb11e50a40 Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Tue, 27 Aug 2024 11:59:49 -0400 Subject: [PATCH] bulk update latest ucsc version and fix failures --- recipes/ucsc-addcols/build.sh | 2 +- recipes/ucsc-addcols/meta.yaml | 5 +- recipes/ucsc-ameme/build.sh | 11 +++-- recipes/ucsc-ameme/meta.yaml | 7 ++- recipes/ucsc-autodtd/build.sh | 11 +++-- recipes/ucsc-autodtd/meta.yaml | 9 ++-- recipes/ucsc-autosql/build.sh | 11 +++-- recipes/ucsc-autosql/meta.yaml | 7 ++- recipes/ucsc-autoxml/build.sh | 11 +++-- recipes/ucsc-autoxml/meta.yaml | 9 ++-- recipes/ucsc-avecols/build.sh | 11 +++-- recipes/ucsc-avecols/meta.yaml | 7 ++- recipes/ucsc-axtchain/build.sh | 28 +++++++---- recipes/ucsc-axtchain/include.patch | 33 ++++--------- recipes/ucsc-axtchain/meta.yaml | 28 +++++++---- recipes/ucsc-axtsort/build.sh | 11 +++-- recipes/ucsc-axtsort/meta.yaml | 9 ++-- recipes/ucsc-axtswap/build.sh | 8 ++-- recipes/ucsc-axtswap/meta.yaml | 9 ++-- recipes/ucsc-axttomaf/build.sh | 28 +++++++---- recipes/ucsc-axttomaf/include.patch | 6 +-- recipes/ucsc-axttomaf/meta.yaml | 29 ++++++++---- recipes/ucsc-axttopsl/build.sh | 28 +++++++---- recipes/ucsc-axttopsl/include.patch | 37 +++++---------- recipes/ucsc-axttopsl/meta.yaml | 28 +++++++---- recipes/ucsc-bamtopsl/build.sh | 28 +++++++---- recipes/ucsc-bamtopsl/include.patch | 6 +-- recipes/ucsc-bamtopsl/meta.yaml | 29 ++++++++---- recipes/ucsc-bedclip/build.sh | 33 +++++++------ recipes/ucsc-bedclip/include.patch | 6 +-- recipes/ucsc-bedclip/meta.yaml | 33 +++++++------ recipes/ucsc-bedcommonregions/build.sh | 11 +++-- recipes/ucsc-bedcommonregions/meta.yaml | 9 ++-- recipes/ucsc-bedcoverage/build.sh | 28 +++++++---- recipes/ucsc-bedcoverage/include.patch | 6 +-- recipes/ucsc-bedcoverage/meta.yaml | 29 ++++++++---- recipes/ucsc-bedextendranges/build.sh | 28 +++++++---- recipes/ucsc-bedextendranges/include.patch | 6 +-- recipes/ucsc-bedextendranges/meta.yaml | 29 ++++++++---- recipes/ucsc-bedgeneparts/build.sh | 11 +++-- recipes/ucsc-bedgeneparts/meta.yaml | 9 ++-- recipes/ucsc-bedgraphpack/build.sh | 10 ++-- recipes/ucsc-bedgraphpack/meta.yaml | 9 ++-- recipes/ucsc-bedgraphtobigwig/build.sh | 28 ++++++----- recipes/ucsc-bedgraphtobigwig/include.patch | 14 +++--- recipes/ucsc-bedgraphtobigwig/meta.yaml | 36 +++++++++------ recipes/ucsc-bedintersect/build.sh | 28 +++++++---- recipes/ucsc-bedintersect/include.patch | 6 +-- recipes/ucsc-bedintersect/meta.yaml | 29 ++++++++---- recipes/ucsc-beditemoverlapcount/build.sh | 28 +++++++---- .../ucsc-beditemoverlapcount/include.patch | 6 +-- recipes/ucsc-beditemoverlapcount/meta.yaml | 29 ++++++++---- recipes/ucsc-bedjointaboffset/build.sh | 9 ++-- recipes/ucsc-bedjointaboffset/include.patch | 6 +-- recipes/ucsc-bedjointaboffset/meta.yaml | 28 +++++++++-- recipes/ucsc-bedpileups/build.sh | 28 +++++++---- recipes/ucsc-bedpileups/include.patch | 6 +-- recipes/ucsc-bedpileups/meta.yaml | 29 ++++++++---- 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recipes/ucsc-rasqlquery/include.patch | 6 +-- recipes/ucsc-rasqlquery/meta.yaml | 29 ++++++++---- recipes/ucsc-ratolines/build.sh | 28 +++++++---- recipes/ucsc-ratolines/include.patch | 6 +-- recipes/ucsc-ratolines/meta.yaml | 29 ++++++++---- recipes/ucsc-ratotab/build.sh | 28 +++++++---- recipes/ucsc-ratotab/include.patch | 6 +-- recipes/ucsc-ratotab/meta.yaml | 29 ++++++++---- recipes/ucsc-rmfadups/build.sh | 28 +++++++---- recipes/ucsc-rmfadups/include.patch | 6 +-- recipes/ucsc-rmfadups/meta.yaml | 29 ++++++++---- recipes/ucsc-rowstocols/build.sh | 28 +++++++---- recipes/ucsc-rowstocols/include.patch | 6 +-- recipes/ucsc-rowstocols/meta.yaml | 29 ++++++++---- recipes/ucsc-spacedtotab/build.sh | 28 +++++++---- recipes/ucsc-spacedtotab/include.patch | 6 +-- recipes/ucsc-spacedtotab/meta.yaml | 29 ++++++++---- recipes/ucsc-splitfile/build.sh | 28 +++++++---- recipes/ucsc-splitfile/include.patch | 6 +-- recipes/ucsc-splitfile/meta.yaml | 29 ++++++++---- recipes/ucsc-splitfilebycolumn/build.sh | 28 +++++++---- recipes/ucsc-splitfilebycolumn/include.patch | 6 +-- recipes/ucsc-splitfilebycolumn/meta.yaml | 29 ++++++++---- recipes/ucsc-sqltoxml/build.sh | 28 +++++++---- recipes/ucsc-sqltoxml/include.patch | 6 +-- recipes/ucsc-sqltoxml/meta.yaml | 29 ++++++++---- recipes/ucsc-stringify/build.sh | 10 ++-- recipes/ucsc-stringify/meta.yaml | 15 +++--- recipes/ucsc-subchar/build.sh | 10 ++-- recipes/ucsc-subchar/meta.yaml | 13 ++++-- recipes/ucsc-subcolumn/build.sh | 28 +++++++---- recipes/ucsc-subcolumn/include.patch | 6 +-- recipes/ucsc-subcolumn/meta.yaml | 29 ++++++++---- recipes/ucsc-taillines/build.sh | 28 +++++++---- recipes/ucsc-taillines/include.patch | 6 +-- recipes/ucsc-taillines/meta.yaml | 29 ++++++++---- recipes/ucsc-tdbquery/build.sh | 28 +++++++---- recipes/ucsc-tdbquery/include.patch | 6 +-- recipes/ucsc-tdbquery/meta.yaml | 29 ++++++++---- recipes/ucsc-texthistogram/build.sh | 28 +++++++---- recipes/ucsc-texthistogram/include.patch | 6 +-- recipes/ucsc-texthistogram/meta.yaml | 29 ++++++++---- recipes/ucsc-ticktodate/build.sh | 28 +++++++---- recipes/ucsc-ticktodate/include.patch | 6 +-- recipes/ucsc-ticktodate/meta.yaml | 29 ++++++++---- recipes/ucsc-tolower/build.sh | 10 ++-- recipes/ucsc-tolower/meta.yaml | 14 +++--- recipes/ucsc-toupper/build.sh | 28 +++++++---- recipes/ucsc-toupper/include.patch | 6 +-- recipes/ucsc-toupper/meta.yaml | 29 ++++++++---- recipes/ucsc-transmappsltogenepred/build.sh | 28 +++++++---- .../ucsc-transmappsltogenepred/include.patch | 6 +-- recipes/ucsc-transmappsltogenepred/meta.yaml | 29 ++++++++---- recipes/ucsc-trfbig/build.sh | 28 +++++++---- recipes/ucsc-trfbig/include.patch | 6 +-- recipes/ucsc-trfbig/meta.yaml | 29 ++++++++---- recipes/ucsc-twobitdup/build.sh | 28 +++++++---- recipes/ucsc-twobitdup/include.patch | 6 +-- recipes/ucsc-twobitdup/meta.yaml | 29 ++++++++---- recipes/ucsc-twobitinfo/build.sh | 28 +++++++---- recipes/ucsc-twobitinfo/include.patch | 26 ++++------- recipes/ucsc-twobitinfo/meta.yaml | 34 +++++++------- recipes/ucsc-twobitmask/build.sh | 28 +++++++---- recipes/ucsc-twobitmask/include.patch | 6 +-- recipes/ucsc-twobitmask/meta.yaml | 29 ++++++++---- recipes/ucsc-twobittofa/build.sh | 26 +++++++---- recipes/ucsc-twobittofa/include.patch | 26 ++++------- recipes/ucsc-twobittofa/meta.yaml | 44 +++++++++--------- recipes/ucsc-validatefiles/build.sh | 28 +++++++---- recipes/ucsc-validatefiles/include.patch | 6 +-- recipes/ucsc-validatefiles/meta.yaml | 29 ++++++++---- recipes/ucsc-validatemanifest/build.sh | 28 +++++++---- recipes/ucsc-validatemanifest/include.patch | 6 +-- recipes/ucsc-validatemanifest/meta.yaml | 29 ++++++++---- recipes/ucsc-websync/build.sh | 9 ++-- recipes/ucsc-websync/include.patch | 6 +-- recipes/ucsc-websync/meta.yaml | 28 +++++++++-- recipes/ucsc-wigcorrelate/build.sh | 28 +++++++---- recipes/ucsc-wigcorrelate/include.patch | 6 +-- recipes/ucsc-wigcorrelate/meta.yaml | 29 ++++++++---- recipes/ucsc-wigtobigwig/build.sh | 28 +++++++---- recipes/ucsc-wigtobigwig/include.patch | 26 ++++------- recipes/ucsc-wigtobigwig/meta.yaml | 44 +++++++++--------- recipes/ucsc-wordline/build.sh | 28 +++++++---- recipes/ucsc-wordline/include.patch | 6 +-- recipes/ucsc-wordline/meta.yaml | 29 ++++++++---- recipes/ucsc-xmlcat/build.sh | 12 ++--- recipes/ucsc-xmlcat/meta.yaml | 13 ++++-- recipes/ucsc-xmltosql/build.sh | 28 +++++++---- recipes/ucsc-xmltosql/include.patch | 6 +-- recipes/ucsc-xmltosql/meta.yaml | 29 ++++++++---- 745 files changed, 9625 insertions(+), 5729 deletions(-) diff --git a/recipes/ucsc-addcols/build.sh b/recipes/ucsc-addcols/build.sh index 1acf16c4e77af..880241ad96660 100644 --- a/recipes/ucsc-addcols/build.sh +++ b/recipes/ucsc-addcols/build.sh @@ -17,5 +17,5 @@ mkdir -p "${BINDIR}" (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/addCols && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/addCols "${PREFIX}/bin" +cp bin/addCols "${PREFIX}/bin" chmod 0755 "${PREFIX}/bin/addCols" diff --git a/recipes/ucsc-addcols/meta.yaml b/recipes/ucsc-addcols/meta.yaml index b192a7574045a..63fadaf3b0f19 100644 --- a/recipes/ucsc-addcols/meta.yaml +++ b/recipes/ucsc-addcols/meta.yaml @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-ameme/build.sh b/recipes/ucsc-ameme/build.sh index 85f44dbbbfe3c..9d9cf92f41ee3 100644 --- a/recipes/ucsc-ameme/build.sh +++ b/recipes/ucsc-ameme/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/ameme && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/ameme "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/ameme" +cp bin/ameme "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/ameme" diff --git a/recipes/ucsc-ameme/meta.yaml b/recipes/ucsc-ameme/meta.yaml index 55193a0bb388c..7b92909aa8ed1 100644 --- a/recipes/ucsc-ameme/meta.yaml +++ b/recipes/ucsc-ameme/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ameme" %} {% set program = "ameme" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-autodtd/build.sh b/recipes/ucsc-autodtd/build.sh index 1f36af8025753..ebab5b497694d 100644 --- a/recipes/ucsc-autodtd/build.sh +++ b/recipes/ucsc-autodtd/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/autoDtd && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/autoDtd "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/autoDtd" +cp bin/autoDtd "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/autoDtd" diff --git a/recipes/ucsc-autodtd/meta.yaml b/recipes/ucsc-autodtd/meta.yaml index e68e033f37830..597fe094769b6 100644 --- a/recipes/ucsc-autodtd/meta.yaml +++ b/recipes/ucsc-autodtd/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-autodtd" %} {% set program = "autoDtd" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-autosql/build.sh b/recipes/ucsc-autosql/build.sh index 9b7d4357f7341..ee0b575e35b97 100644 --- a/recipes/ucsc-autosql/build.sh +++ b/recipes/ucsc-autosql/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/autoSql && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/autoSql "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/autoSql" +cp bin/autoSql "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/autoSql" diff --git a/recipes/ucsc-autosql/meta.yaml b/recipes/ucsc-autosql/meta.yaml index 87e2d555f0df2..b2a651b3b5a58 100644 --- a/recipes/ucsc-autosql/meta.yaml +++ b/recipes/ucsc-autosql/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-autosql" %} {% set program = "autoSql" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-autoxml/build.sh b/recipes/ucsc-autoxml/build.sh index 5476f6f1d0a83..73dfe37c83820 100644 --- a/recipes/ucsc-autoxml/build.sh +++ b/recipes/ucsc-autoxml/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/autoXml && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/autoXml "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/autoXml" +cp bin/autoXml "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/autoXml" diff --git a/recipes/ucsc-autoxml/meta.yaml b/recipes/ucsc-autoxml/meta.yaml index 9c3792b8558d4..c5328653b9315 100644 --- a/recipes/ucsc-autoxml/meta.yaml +++ b/recipes/ucsc-autoxml/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-autoxml" %} {% set program = "autoXml" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-avecols/build.sh b/recipes/ucsc-avecols/build.sh index b9727be3692ee..eb3ce0613441f 100644 --- a/recipes/ucsc-avecols/build.sh +++ b/recipes/ucsc-avecols/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/aveCols && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/aveCols "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/aveCols" +cp bin/aveCols "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/aveCols" diff --git a/recipes/ucsc-avecols/meta.yaml b/recipes/ucsc-avecols/meta.yaml index 0d1e71052c40e..1845792fc30ac 100644 --- a/recipes/ucsc-avecols/meta.yaml +++ b/recipes/ucsc-avecols/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-avecols" %} {% set program = "aveCols" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-axtchain/build.sh b/recipes/ucsc-axtchain/build.sh index 0cf99f309dc17..1765bb92a55e3 100644 --- a/recipes/ucsc-axtchain/build.sh +++ b/recipes/ucsc-axtchain/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/axtChain && make) -cp bin/axtChain "$PREFIX/bin" -chmod +x "$PREFIX/bin/axtChain" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/axtChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/axtChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtChain" diff --git a/recipes/ucsc-axtchain/include.patch b/recipes/ucsc-axtchain/include.patch index e4831ef2dea13..edc04d0dc2f64 100644 --- a/recipes/ucsc-axtchain/include.patch +++ b/recipes/ucsc-axtchain/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-axtchain/meta.yaml b/recipes/ucsc-axtchain/meta.yaml index 72064fd875b92..8bdb49a164a0d 100644 --- a/recipes/ucsc-axtchain/meta.yaml +++ b/recipes/ucsc-axtchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtchain" %} {% set program = "axtChain" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Chain together axt alignments." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-axtsort/build.sh b/recipes/ucsc-axtsort/build.sh index 496cf5dcb35d8..f8296a72424f0 100644 --- a/recipes/ucsc-axtsort/build.sh +++ b/recipes/ucsc-axtsort/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/mouseStuff/axtSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/axtSort "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/axtSort" +cp bin/axtSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtSort" diff --git a/recipes/ucsc-axtsort/meta.yaml b/recipes/ucsc-axtsort/meta.yaml index 4c4b3f7e611c5..41b575334e20f 100644 --- a/recipes/ucsc-axtsort/meta.yaml +++ b/recipes/ucsc-axtsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtsort" %} {% set program = "axtSort" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-axtswap/build.sh b/recipes/ucsc-axtswap/build.sh index c15f336ce33a1..002d003249880 100644 --- a/recipes/ucsc-axtswap/build.sh +++ b/recipes/ucsc-axtswap/build.sh @@ -2,7 +2,7 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -11,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/mouseStuff/axtSwap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/axtSwap "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/axtSwap" +cp bin/axtSwap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtSwap" diff --git a/recipes/ucsc-axtswap/meta.yaml b/recipes/ucsc-axtswap/meta.yaml index a432cdd091d15..af74691f328d2 100644 --- a/recipes/ucsc-axtswap/meta.yaml +++ b/recipes/ucsc-axtswap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axtswap" %} {% set program = "axtSwap" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-axttomaf/build.sh b/recipes/ucsc-axttomaf/build.sh index 9b86c892dc16a..8aff3ba3ee73e 100644 --- a/recipes/ucsc-axttomaf/build.sh +++ b/recipes/ucsc-axttomaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/axtToMaf && make) -cp bin/axtToMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/axtToMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/axtToMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/axtToMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtToMaf" diff --git a/recipes/ucsc-axttomaf/include.patch b/recipes/ucsc-axttomaf/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-axttomaf/include.patch +++ b/recipes/ucsc-axttomaf/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-axttomaf/meta.yaml b/recipes/ucsc-axttomaf/meta.yaml index c4c3506781e5f..9fad27f9b6c48 100644 --- a/recipes/ucsc-axttomaf/meta.yaml +++ b/recipes/ucsc-axttomaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axttomaf" %} {% set program = "axtToMaf" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from axt to maf format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-axttopsl/build.sh b/recipes/ucsc-axttopsl/build.sh index d34c31e9c40dd..53d90bfeef68a 100644 --- a/recipes/ucsc-axttopsl/build.sh +++ b/recipes/ucsc-axttopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/axtToPsl && make) -cp bin/axtToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/axtToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/axtToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/axtToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/axtToPsl" diff --git a/recipes/ucsc-axttopsl/include.patch b/recipes/ucsc-axttopsl/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-axttopsl/include.patch +++ b/recipes/ucsc-axttopsl/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-axttopsl/meta.yaml b/recipes/ucsc-axttopsl/meta.yaml index d3c5108e5d1c7..b6873169ffcc3 100644 --- a/recipes/ucsc-axttopsl/meta.yaml +++ b/recipes/ucsc-axttopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-axttopsl" %} {% set program = "axtToPsl" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert axt to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bamtopsl/build.sh b/recipes/ucsc-bamtopsl/build.sh index ce701d375c18f..c68078409abcb 100644 --- a/recipes/ucsc-bamtopsl/build.sh +++ b/recipes/ucsc-bamtopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bamToPsl && make) -cp bin/bamToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/bamToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bamToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bamToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bamToPsl" diff --git a/recipes/ucsc-bamtopsl/include.patch b/recipes/ucsc-bamtopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bamtopsl/include.patch +++ b/recipes/ucsc-bamtopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bamtopsl/meta.yaml b/recipes/ucsc-bamtopsl/meta.yaml index 3ab6ea6912eda..24249d39cd741 100644 --- a/recipes/ucsc-bamtopsl/meta.yaml +++ b/recipes/ucsc-bamtopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bamtopsl" %} {% set program = "bamToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 3 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert a bam file to a psl and optionally also a fasta file that contains the reads." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedclip/build.sh b/recipes/ucsc-bedclip/build.sh index a0d9457e75286..7899ca0c8a07a 100644 --- a/recipes/ucsc-bedclip/build.sh +++ b/recipes/ucsc-bedclip/build.sh @@ -1,22 +1,21 @@ #!/bin/bash -if [ $(arch) = "aarch64" ] -then - export CFLAGS+=" -O3 " - export CPPFLAGS+=" -O3 " -else - export MACHTYPE=x86_64 -fi +set -xe +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" - -mkdir -p "$PREFIX/bin" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedClip && make) -cp bin/bedClip "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedClip" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedClip && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedClip "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedClip" diff --git a/recipes/ucsc-bedclip/include.patch b/recipes/ucsc-bedclip/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedclip/include.patch +++ b/recipes/ucsc-bedclip/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml index b985207becc8a..3dcd15559784f 100644 --- a/recipes/ucsc-bedclip/meta.yaml +++ b/recipes/ucsc-bedclip/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedclip" %} {% set program = "bedClip" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -12,13 +12,12 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" - - "patch1.patch" build: skip: True # [osx] - number: 4 + number: 0 run_exports: - - {{ pin_subpackage("ucsc-bedclip", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -28,25 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} + +about: + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Remove lines from bed file that refer to off-chromosome locations." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 - -about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Remove lines from bed file that refer to off-chromosome locations." diff --git a/recipes/ucsc-bedcommonregions/build.sh b/recipes/ucsc-bedcommonregions/build.sh index 2ec002da3d943..8184ab80f550d 100644 --- a/recipes/ucsc-bedcommonregions/build.sh +++ b/recipes/ucsc-bedcommonregions/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedCommonRegions && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedCommonRegions "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedCommonRegions" +cp bin/bedCommonRegions "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedCommonRegions" diff --git a/recipes/ucsc-bedcommonregions/meta.yaml b/recipes/ucsc-bedcommonregions/meta.yaml index 78698cd3f1e32..7e61e49095f09 100644 --- a/recipes/ucsc-bedcommonregions/meta.yaml +++ b/recipes/ucsc-bedcommonregions/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedcommonregions" %} {% set program = "bedCommonRegions" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedcoverage/build.sh b/recipes/ucsc-bedcoverage/build.sh index e7cb194b48474..d9dd530db9deb 100644 --- a/recipes/ucsc-bedcoverage/build.sh +++ b/recipes/ucsc-bedcoverage/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/bedCoverage && make) -cp bin/bedCoverage "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedCoverage" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/bedCoverage && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedCoverage "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedCoverage" diff --git a/recipes/ucsc-bedcoverage/include.patch b/recipes/ucsc-bedcoverage/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedcoverage/include.patch +++ b/recipes/ucsc-bedcoverage/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedcoverage/meta.yaml b/recipes/ucsc-bedcoverage/meta.yaml index ec874780ff0ec..674998459671f 100644 --- a/recipes/ucsc-bedcoverage/meta.yaml +++ b/recipes/ucsc-bedcoverage/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedcoverage" %} {% set program = "bedCoverage" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Analyse coverage by bed files - chromosome by " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedextendranges/build.sh b/recipes/ucsc-bedextendranges/build.sh index f136ad15518a5..7027ce1284eba 100644 --- a/recipes/ucsc-bedextendranges/build.sh +++ b/recipes/ucsc-bedextendranges/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/bedExtendRanges && make) -cp bin/bedExtendRanges "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedExtendRanges" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bedExtendRanges && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedExtendRanges "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedExtendRanges" diff --git a/recipes/ucsc-bedextendranges/include.patch b/recipes/ucsc-bedextendranges/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedextendranges/include.patch +++ b/recipes/ucsc-bedextendranges/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedextendranges/meta.yaml b/recipes/ucsc-bedextendranges/meta.yaml index 8b388ba115445..99ea4fdb29f6e 100644 --- a/recipes/ucsc-bedextendranges/meta.yaml +++ b/recipes/ucsc-bedextendranges/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedextendranges" %} {% set program = "bedExtendRanges" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "extend length of entries in bed 6+ data to be at least the given length," + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedgeneparts/build.sh b/recipes/ucsc-bedgeneparts/build.sh index f1399eb250589..c1d170f184800 100644 --- a/recipes/ucsc-bedgeneparts/build.sh +++ b/recipes/ucsc-bedgeneparts/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedGeneParts && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedGeneParts "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedGeneParts" +cp bin/bedGeneParts "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedGeneParts" diff --git a/recipes/ucsc-bedgeneparts/meta.yaml b/recipes/ucsc-bedgeneparts/meta.yaml index 8685b3fe9e52b..de9f72681bcd3 100644 --- a/recipes/ucsc-bedgeneparts/meta.yaml +++ b/recipes/ucsc-bedgeneparts/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedgeneparts" %} {% set program = "bedGeneParts" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedgraphpack/build.sh b/recipes/ucsc-bedgraphpack/build.sh index 35f9f4a4071a5..3600d25ac86be 100644 --- a/recipes/ucsc-bedgraphpack/build.sh +++ b/recipes/ucsc-bedgraphpack/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedGraphPack && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedGraphPack "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedGraphPack" +cp bin/bedGraphPack "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedGraphPack" diff --git a/recipes/ucsc-bedgraphpack/meta.yaml b/recipes/ucsc-bedgraphpack/meta.yaml index 81da67b2ef311..d950f7ed9e88e 100644 --- a/recipes/ucsc-bedgraphpack/meta.yaml +++ b/recipes/ucsc-bedgraphpack/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedgraphpack" %} {% set program = "bedGraphPack" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedgraphtobigwig/build.sh b/recipes/ucsc-bedgraphtobigwig/build.sh index a41225d70c23a..5d7368f71bdd2 100644 --- a/recipes/ucsc-bedgraphtobigwig/build.sh +++ b/recipes/ucsc-bedgraphtobigwig/build.sh @@ -1,17 +1,21 @@ #!/bin/bash + +set -xe + mkdir -p "${PREFIX}/bin" -export MACHTYPE=x86_64 -export BINDIR=`pwd`/bin +export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" -export LD_LIBRARY_PATH="${PREFIX}/lib" -export LDFLAGS="-L${PREFIX}/lib" -export CFLAGS="-I${PREFIX}/include ${LDFLAGS}" -export CXXFLAGS="-I${PREFIX}/include ${LDFLAGS}" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" mkdir -p "${BINDIR}" -cd ${SRC_DIR}/kent/src/lib && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cd ${SRC_DIR}/kent/src/htslib && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cd ${SRC_DIR}/kent/src/jkOwnLib && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cd ${SRC_DIR}/kent/src/utils/bedGraphToBigWig && make CC=${CC} CXX=${CXX} CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -cp ${SRC_DIR}/bin/bedGraphToBigWig "${PREFIX}/bin" -chmod +x "${PREFIX}/bin/bedGraphToBigWig" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedGraphToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedGraphToBigWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedGraphToBigWig" diff --git a/recipes/ucsc-bedgraphtobigwig/include.patch b/recipes/ucsc-bedgraphtobigwig/include.patch index b4b153480032c..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedgraphtobigwig/include.patch +++ b/recipes/ucsc-bedgraphtobigwig/include.patch @@ -1,24 +1,24 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index 9aec6cf66f7a4..ea2f56db02e67 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -1,21 +1,21 @@ {% set package = "ucsc-bedgraphtobigwig" %} {% set program = "bedGraphToBigWig" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" version: "{{ version }}" source: - url: "https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" sha256: "{{ sha256 }}" patches: - "include.patch" - - "patch1.patch" build: - number: 1 + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -23,29 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - - openssl - zlib + run: - libpng - libuuid - - openssl + - mysql-connector-c + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} + +about: + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert a bedGraph file to bigWig format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 - -about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert a bedGraph file to bigWig format." diff --git a/recipes/ucsc-bedintersect/build.sh b/recipes/ucsc-bedintersect/build.sh index 463e5ef29d12d..e8735ba8125e6 100644 --- a/recipes/ucsc-bedintersect/build.sh +++ b/recipes/ucsc-bedintersect/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/bedIntersect && make) -cp bin/bedIntersect "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedIntersect" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/bedIntersect && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedIntersect "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedIntersect" diff --git a/recipes/ucsc-bedintersect/include.patch b/recipes/ucsc-bedintersect/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedintersect/include.patch +++ b/recipes/ucsc-bedintersect/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedintersect/meta.yaml b/recipes/ucsc-bedintersect/meta.yaml index 8f70102146641..5ed61c6ad927f 100644 --- a/recipes/ucsc-bedintersect/meta.yaml +++ b/recipes/ucsc-bedintersect/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedintersect" %} {% set program = "bedIntersect" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Intersect two bed files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-beditemoverlapcount/build.sh b/recipes/ucsc-beditemoverlapcount/build.sh index bfb85d4baf7e3..9e731e0e7b060 100644 --- a/recipes/ucsc-beditemoverlapcount/build.sh +++ b/recipes/ucsc-beditemoverlapcount/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/bedItemOverlapCount && make) -cp bin/bedItemOverlapCount "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedItemOverlapCount" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/bedItemOverlapCount && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedItemOverlapCount "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedItemOverlapCount" diff --git a/recipes/ucsc-beditemoverlapcount/include.patch b/recipes/ucsc-beditemoverlapcount/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-beditemoverlapcount/include.patch +++ b/recipes/ucsc-beditemoverlapcount/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-beditemoverlapcount/meta.yaml b/recipes/ucsc-beditemoverlapcount/meta.yaml index 5fa66226d97c3..b9ba99ef82232 100644 --- a/recipes/ucsc-beditemoverlapcount/meta.yaml +++ b/recipes/ucsc-beditemoverlapcount/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-beditemoverlapcount" %} {% set program = "bedItemOverlapCount" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "count number of times a base is overlapped by the" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedjointaboffset/build.sh b/recipes/ucsc-bedjointaboffset/build.sh index b0fa55386a339..66c35a7548a83 100644 --- a/recipes/ucsc-bedjointaboffset/build.sh +++ b/recipes/ucsc-bedjointaboffset/build.sh @@ -1,4 +1,7 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -cp kent/src/utils/bedJoinTabOffset "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedJoinTabOffset" + +set -xe + +mkdir -p "${PREFIX}/bin" +cp kent/src/utils/bedJoinTabOffset "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedJoinTabOffset" diff --git a/recipes/ucsc-bedjointaboffset/include.patch b/recipes/ucsc-bedjointaboffset/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedjointaboffset/include.patch +++ b/recipes/ucsc-bedjointaboffset/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedjointaboffset/meta.yaml b/recipes/ucsc-bedjointaboffset/meta.yaml index 5fb1d736c7504..4b240b97ec0ee 100644 --- a/recipes/ucsc-bedjointaboffset/meta.yaml +++ b/recipes/ucsc-bedjointaboffset/meta.yaml @@ -1,30 +1,39 @@ {% set package = "ucsc-bedjointaboffset" %} {% set program = "bedJoinTabOffset" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" version: "{{ version }}" source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{ version }.src.tgz" sha256: "{{ sha256 }}" patches: - "include.patch" build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - { pin_subpackage(package, max_pin=None) } requirements: build: + - {{ compiler('c') }} host: + - libpng + - libuuid + - mysql-connector-c + - libopenssl-static + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -37,3 +46,12 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "given a bed file and tab file where each have a column with matching values: first get the value of column0, the offset and line length from inTabFile. Then go over the bed file, use the name field and append its offset and length to the bed file as two separate fields. Write the new bed file to outBed." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedpileups/build.sh b/recipes/ucsc-bedpileups/build.sh index f1aa76b9a3b4c..d49b45360aa4d 100644 --- a/recipes/ucsc-bedpileups/build.sh +++ b/recipes/ucsc-bedpileups/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedPileUps && make) -cp bin/bedPileUps "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedPileUps" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedPileUps && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedPileUps "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedPileUps" diff --git a/recipes/ucsc-bedpileups/include.patch b/recipes/ucsc-bedpileups/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedpileups/include.patch +++ b/recipes/ucsc-bedpileups/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedpileups/meta.yaml b/recipes/ucsc-bedpileups/meta.yaml index b3e70a97e2c18..f75c721a2889f 100644 --- a/recipes/ucsc-bedpileups/meta.yaml +++ b/recipes/ucsc-bedpileups/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedpileups" %} {% set program = "bedPileUps" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Find (exact) overlaps if any in bed input" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedremoveoverlap/build.sh b/recipes/ucsc-bedremoveoverlap/build.sh index 971f4a5ace1d1..ee59fd0ba4298 100644 --- a/recipes/ucsc-bedremoveoverlap/build.sh +++ b/recipes/ucsc-bedremoveoverlap/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bedRemoveOverlap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedRemoveOverlap "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedRemoveOverlap" +cp bin/bedRemoveOverlap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedRemoveOverlap" diff --git a/recipes/ucsc-bedremoveoverlap/meta.yaml b/recipes/ucsc-bedremoveoverlap/meta.yaml index a35d8341dbdbd..40e11ffca0e67 100644 --- a/recipes/ucsc-bedremoveoverlap/meta.yaml +++ b/recipes/ucsc-bedremoveoverlap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedremoveoverlap" %} {% set program = "bedRemoveOverlap" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedrestricttopositions/build.sh b/recipes/ucsc-bedrestricttopositions/build.sh index e27e6ecc54f19..82f7323e39f3d 100644 --- a/recipes/ucsc-bedrestricttopositions/build.sh +++ b/recipes/ucsc-bedrestricttopositions/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedRestrictToPositions && make) -cp bin/bedRestrictToPositions "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedRestrictToPositions" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedRestrictToPositions && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedRestrictToPositions "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedRestrictToPositions" diff --git a/recipes/ucsc-bedrestricttopositions/include.patch b/recipes/ucsc-bedrestricttopositions/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedrestricttopositions/include.patch +++ b/recipes/ucsc-bedrestricttopositions/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedrestricttopositions/meta.yaml b/recipes/ucsc-bedrestricttopositions/meta.yaml index 1c9117bdb25e3..ab068a46f57fb 100644 --- a/recipes/ucsc-bedrestricttopositions/meta.yaml +++ b/recipes/ucsc-bedrestricttopositions/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedrestricttopositions" %} {% set program = "bedRestrictToPositions" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedsort/build.sh b/recipes/ucsc-bedsort/build.sh index 7a161baafe158..308bd9a232ed2 100644 --- a/recipes/ucsc-bedsort/build.sh +++ b/recipes/ucsc-bedsort/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/bedSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedSort "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedSort" +cp bin/bedSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedSort" diff --git a/recipes/ucsc-bedsort/include.patch b/recipes/ucsc-bedsort/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedsort/include.patch +++ b/recipes/ucsc-bedsort/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedsort/meta.yaml b/recipes/ucsc-bedsort/meta.yaml index 832d257a70c12..416d0f783723e 100644 --- a/recipes/ucsc-bedsort/meta.yaml +++ b/recipes/ucsc-bedsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedsort" %} {% set program = "bedSort" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,9 +14,10 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-bedsort', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -28,11 +29,13 @@ requirements: - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -41,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Sort a .bed file by chrom,chromStart" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-bedtobigbed/build.sh b/recipes/ucsc-bedtobigbed/build.sh index fb722163f7ad1..2b2c5a16aad45 100644 --- a/recipes/ucsc-bedtobigbed/build.sh +++ b/recipes/ucsc-bedtobigbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/bedToBigBed && make) -cp bin/bedToBigBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedToBigBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bedToBigBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedToBigBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedToBigBed" diff --git a/recipes/ucsc-bedtobigbed/include.patch b/recipes/ucsc-bedtobigbed/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedtobigbed/include.patch +++ b/recipes/ucsc-bedtobigbed/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bedtobigbed/meta.yaml b/recipes/ucsc-bedtobigbed/meta.yaml index dc6ece24ed64b..156f4100092c2 100644 --- a/recipes/ucsc-bedtobigbed/meta.yaml +++ b/recipes/ucsc-bedtobigbed/meta.yaml @@ -1,25 +1,21 @@ {% set package = "ucsc-bedtobigbed" %} {% set program = "bedToBigBed" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert bed file to bigBed. (bbi version: 4)" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert bed file to bigBed. (BigBed version: 4)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedtogenepred/build.sh b/recipes/ucsc-bedtogenepred/build.sh index aa966fdb34201..163f8a5c60726 100644 --- a/recipes/ucsc-bedtogenepred/build.sh +++ b/recipes/ucsc-bedtogenepred/build.sh @@ -1,21 +1,21 @@ #!/bin/bash -set -xe +set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p $BINDIR +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/bedToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bedToGenePred "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bedToGenePred" +cp bin/bedToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedToGenePred" diff --git a/recipes/ucsc-bedtogenepred/meta.yaml b/recipes/ucsc-bedtogenepred/meta.yaml index 0e5ba571827a5..34b1da3e05faa 100644 --- a/recipes/ucsc-bedtogenepred/meta.yaml +++ b/recipes/ucsc-bedtogenepred/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedtogenepred" %} {% set program = "bedToGenePred" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: -# - linux-aarch64 # linking fails with `undefined reference to `cram_get_Md5'` and few more functions \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bedtopsl/build.sh b/recipes/ucsc-bedtopsl/build.sh index dcab9d7776a97..27fed78f2e79a 100644 --- a/recipes/ucsc-bedtopsl/build.sh +++ b/recipes/ucsc-bedtopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/bedToPsl && make) -cp bin/bedToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bedToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedToPsl" diff --git a/recipes/ucsc-bedtopsl/include.patch b/recipes/ucsc-bedtopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedtopsl/include.patch +++ b/recipes/ucsc-bedtopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedtopsl/meta.yaml b/recipes/ucsc-bedtopsl/meta.yaml index 07b6858631fe6..bf6d5446c806b 100644 --- a/recipes/ucsc-bedtopsl/meta.yaml +++ b/recipes/ucsc-bedtopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedtopsl" %} {% set program = "bedToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert bed format files to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bedweedoverlapping/build.sh b/recipes/ucsc-bedweedoverlapping/build.sh index 002beb540c1dd..08ebc84a92e93 100644 --- a/recipes/ucsc-bedweedoverlapping/build.sh +++ b/recipes/ucsc-bedweedoverlapping/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/bedWeedOverlapping && make) -cp bin/bedWeedOverlapping "$PREFIX/bin" -chmod +x "$PREFIX/bin/bedWeedOverlapping" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bedWeedOverlapping && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bedWeedOverlapping "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bedWeedOverlapping" diff --git a/recipes/ucsc-bedweedoverlapping/include.patch b/recipes/ucsc-bedweedoverlapping/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-bedweedoverlapping/include.patch +++ b/recipes/ucsc-bedweedoverlapping/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bedweedoverlapping/meta.yaml b/recipes/ucsc-bedweedoverlapping/meta.yaml index bc6676b987bb3..e372114ed5e4b 100644 --- a/recipes/ucsc-bedweedoverlapping/meta.yaml +++ b/recipes/ucsc-bedweedoverlapping/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bedweedoverlapping" %} {% set program = "bedWeedOverlapping" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter out beds that overlap a 'weed.bed' file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-bigbedinfo/build.sh b/recipes/ucsc-bigbedinfo/build.sh index 15cf1c6b82b8a..420bee013e254 100644 --- a/recipes/ucsc-bigbedinfo/build.sh +++ b/recipes/ucsc-bigbedinfo/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedInfo && make -j ${CPU_COUNT}) -cp bin/bigBedInfo "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedInfo" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedInfo "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedInfo" diff --git a/recipes/ucsc-bigbedinfo/include.patch b/recipes/ucsc-bigbedinfo/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbedinfo/include.patch +++ b/recipes/ucsc-bigbedinfo/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbedinfo/meta.yaml b/recipes/ucsc-bigbedinfo/meta.yaml index 93110c41fe8eb..964aa7c634c8e 100644 --- a/recipes/ucsc-bigbedinfo/meta.yaml +++ b/recipes/ucsc-bigbedinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbedinfo" %} {% set program = "bigBedInfo" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Show information about a bigBed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigbednameditems/build.sh b/recipes/ucsc-bigbednameditems/build.sh index 3d04dd5bf568e..777c54b464f56 100644 --- a/recipes/ucsc-bigbednameditems/build.sh +++ b/recipes/ucsc-bigbednameditems/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedNamedItems && make -j ${CPU_COUNT}) -cp bin/bigBedNamedItems "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedNamedItems" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedNamedItems && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedNamedItems "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedNamedItems" diff --git a/recipes/ucsc-bigbednameditems/include.patch b/recipes/ucsc-bigbednameditems/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbednameditems/include.patch +++ b/recipes/ucsc-bigbednameditems/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbednameditems/meta.yaml b/recipes/ucsc-bigbednameditems/meta.yaml index c3514f0bfc7ae..eb9e9631ab382 100644 --- a/recipes/ucsc-bigbednameditems/meta.yaml +++ b/recipes/ucsc-bigbednameditems/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbednameditems" %} {% set program = "bigBedNamedItems" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract item of given name from bigBed" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigbedsummary/build.sh b/recipes/ucsc-bigbedsummary/build.sh index cfb822b0daef1..89e7a9c76ffeb 100644 --- a/recipes/ucsc-bigbedsummary/build.sh +++ b/recipes/ucsc-bigbedsummary/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedSummary && make -j ${CPU_COUNT}) -cp bin/bigBedSummary "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedSummary" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedSummary && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedSummary "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedSummary" diff --git a/recipes/ucsc-bigbedsummary/include.patch b/recipes/ucsc-bigbedsummary/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbedsummary/include.patch +++ b/recipes/ucsc-bigbedsummary/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbedsummary/meta.yaml b/recipes/ucsc-bigbedsummary/meta.yaml index 5a3a07fb3aa8c..528d9716a3817 100644 --- a/recipes/ucsc-bigbedsummary/meta.yaml +++ b/recipes/ucsc-bigbedsummary/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbedsummary" %} {% set program = "bigBedSummary" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract summary information from a bigBed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigbedtobed/build.sh b/recipes/ucsc-bigbedtobed/build.sh index 557d263987d51..dea44fa59530b 100644 --- a/recipes/ucsc-bigbedtobed/build.sh +++ b/recipes/ucsc-bigbedtobed/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigBedToBed && make -j ${CPU_COUNT}) -cp bin/bigBedToBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigBedToBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigBedToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigBedToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigBedToBed" diff --git a/recipes/ucsc-bigbedtobed/include.patch b/recipes/ucsc-bigbedtobed/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigbedtobed/include.patch +++ b/recipes/ucsc-bigbedtobed/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigbedtobed/meta.yaml b/recipes/ucsc-bigbedtobed/meta.yaml index 2572fb5c4f7a8..708bb43118bd2 100644 --- a/recipes/ucsc-bigbedtobed/meta.yaml +++ b/recipes/ucsc-bigbedtobed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigbedtobed" %} {% set program = "bigBedToBed" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,7 +23,6 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid @@ -44,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from bigBed to ascii bed format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigmaftomaf/build.sh b/recipes/ucsc-bigmaftomaf/build.sh index 291b1bb07748e..fbed7ad379763 100644 --- a/recipes/ucsc-bigmaftomaf/build.sh +++ b/recipes/ucsc-bigmaftomaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/bigMafToMaf && make -j ${CPU_COUNT}) -cp bin/bigMafToMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigMafToMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bigMafToMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigMafToMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigMafToMaf" diff --git a/recipes/ucsc-bigmaftomaf/include.patch b/recipes/ucsc-bigmaftomaf/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigmaftomaf/include.patch +++ b/recipes/ucsc-bigmaftomaf/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigmaftomaf/meta.yaml b/recipes/ucsc-bigmaftomaf/meta.yaml index 08fb94982d426..f59a7e70f7d81 100644 --- a/recipes/ucsc-bigmaftomaf/meta.yaml +++ b/recipes/ucsc-bigmaftomaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigmaftomaf" %} {% set program = "bigMafToMaf" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert bigMaf to maf file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigpsltopsl/build.sh b/recipes/ucsc-bigpsltopsl/build.sh index f6e9e3b240bef..ea6e4221c1466 100644 --- a/recipes/ucsc-bigpsltopsl/build.sh +++ b/recipes/ucsc-bigpsltopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/bigPslToPsl && make -j ${CPU_COUNT}) -cp bin/bigPslToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigPslToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/bigPslToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigPslToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigPslToPsl" diff --git a/recipes/ucsc-bigpsltopsl/include.patch b/recipes/ucsc-bigpsltopsl/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigpsltopsl/include.patch +++ b/recipes/ucsc-bigpsltopsl/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigpsltopsl/meta.yaml b/recipes/ucsc-bigpsltopsl/meta.yaml index d8b8df1c6ec46..515aa553be985 100644 --- a/recipes/ucsc-bigpsltopsl/meta.yaml +++ b/recipes/ucsc-bigpsltopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigpsltopsl" %} {% set program = "bigPslToPsl" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert bigPsl file to psl" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigaverageoverbed/build.sh b/recipes/ucsc-bigwigaverageoverbed/build.sh index 36ed74547fa9e..9044dbe5feb95 100644 --- a/recipes/ucsc-bigwigaverageoverbed/build.sh +++ b/recipes/ucsc-bigwigaverageoverbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigAverageOverBed && make -j ${CPU_COUNT}) -cp bin/bigWigAverageOverBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigAverageOverBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigAverageOverBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigAverageOverBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigAverageOverBed" diff --git a/recipes/ucsc-bigwigaverageoverbed/include.patch b/recipes/ucsc-bigwigaverageoverbed/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigaverageoverbed/include.patch +++ b/recipes/ucsc-bigwigaverageoverbed/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigaverageoverbed/meta.yaml b/recipes/ucsc-bigwigaverageoverbed/meta.yaml index a3d7862dd2f63..e2e1bb8da3cce 100644 --- a/recipes/ucsc-bigwigaverageoverbed/meta.yaml +++ b/recipes/ucsc-bigwigaverageoverbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigaverageoverbed" %} {% set program = "bigWigAverageOverBed" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Compute average score of big wig over each bed, which may have introns." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigcat/build.sh b/recipes/ucsc-bigwigcat/build.sh index de0b41cfd02d2..c76176d286e9f 100644 --- a/recipes/ucsc-bigwigcat/build.sh +++ b/recipes/ucsc-bigwigcat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigCat && make -j ${CPU_COUNT}) -cp bin/bigWigCat "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigCat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigCat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigCat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigCat" diff --git a/recipes/ucsc-bigwigcat/include.patch b/recipes/ucsc-bigwigcat/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigcat/include.patch +++ b/recipes/ucsc-bigwigcat/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigcat/meta.yaml b/recipes/ucsc-bigwigcat/meta.yaml index 17562ee0872e2..f314a3ed65b9a 100644 --- a/recipes/ucsc-bigwigcat/meta.yaml +++ b/recipes/ucsc-bigwigcat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigcat" %} {% set program = "bigWigCat" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "merge non-overlapping bigWig files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigcluster/build.sh b/recipes/ucsc-bigwigcluster/build.sh index 765d6480a8b74..dfff70dd0b0a7 100644 --- a/recipes/ucsc-bigwigcluster/build.sh +++ b/recipes/ucsc-bigwigcluster/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigCluster && make -j ${CPU_COUNT}) -cp bin/bigWigCluster "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigCluster" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigCluster && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigCluster "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigCluster" diff --git a/recipes/ucsc-bigwigcluster/include.patch b/recipes/ucsc-bigwigcluster/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigcluster/include.patch +++ b/recipes/ucsc-bigwigcluster/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigcluster/meta.yaml b/recipes/ucsc-bigwigcluster/meta.yaml index 850d0384ba104..b385ad7c28da7 100644 --- a/recipes/ucsc-bigwigcluster/meta.yaml +++ b/recipes/ucsc-bigwigcluster/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigcluster" %} {% set program = "bigWigCluster" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Cluster bigWigs using a hacTree" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigcorrelate/build.sh b/recipes/ucsc-bigwigcorrelate/build.sh index 0d57ea8b1e3de..f4b5ede22c371 100644 --- a/recipes/ucsc-bigwigcorrelate/build.sh +++ b/recipes/ucsc-bigwigcorrelate/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigCorrelate && make -j ${CPU_COUNT}) -cp bin/bigWigCorrelate "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigCorrelate" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigCorrelate && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigCorrelate "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigCorrelate" diff --git a/recipes/ucsc-bigwigcorrelate/include.patch b/recipes/ucsc-bigwigcorrelate/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigcorrelate/include.patch +++ b/recipes/ucsc-bigwigcorrelate/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-bigwigcorrelate/meta.yaml b/recipes/ucsc-bigwigcorrelate/meta.yaml index 069403ca75dcb..0b51d8e1375da 100644 --- a/recipes/ucsc-bigwigcorrelate/meta.yaml +++ b/recipes/ucsc-bigwigcorrelate/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigcorrelate" %} {% set program = "bigWigCorrelate" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Correlate bigWig files, optionally only on target regions." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwiginfo/build.sh b/recipes/ucsc-bigwiginfo/build.sh index 70406d184f47e..6a25548f42c46 100644 --- a/recipes/ucsc-bigwiginfo/build.sh +++ b/recipes/ucsc-bigwiginfo/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bigWigInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bigWigInfo "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bigWigInfo" +cp bin/bigWigInfo "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigInfo" diff --git a/recipes/ucsc-bigwiginfo/include.patch b/recipes/ucsc-bigwiginfo/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwiginfo/include.patch +++ b/recipes/ucsc-bigwiginfo/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-bigwiginfo/meta.yaml b/recipes/ucsc-bigwiginfo/meta.yaml index e338cf6643131..844216cdcde7e 100644 --- a/recipes/ucsc-bigwiginfo/meta.yaml +++ b/recipes/ucsc-bigwiginfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwiginfo" %} {% set program = "bigWigInfo" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,6 +14,7 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -28,11 +29,13 @@ requirements: - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -41,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Print out information about bigWig file." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-bigwigmerge/build.sh b/recipes/ucsc-bigwigmerge/build.sh index 370567ebeae32..c2f18065057b5 100644 --- a/recipes/ucsc-bigwigmerge/build.sh +++ b/recipes/ucsc-bigwigmerge/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/bigWigMerge && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/bigWigMerge "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/bigWigMerge" +cp bin/bigWigMerge "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigMerge" diff --git a/recipes/ucsc-bigwigmerge/meta.yaml b/recipes/ucsc-bigwigmerge/meta.yaml index f640285ef59b8..96f88d832b3ee 100644 --- a/recipes/ucsc-bigwigmerge/meta.yaml +++ b/recipes/ucsc-bigwigmerge/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-bigwigmerge" %} {% set program = "bigWigMerge" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -19,7 +19,6 @@ build: run_exports: - {{ pin_subpackage(package, max_pin=None) }} - requirements: build: - make @@ -44,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Merge together multiple bigWigs into a single output bedGraph." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigsummary/build.sh b/recipes/ucsc-bigwigsummary/build.sh index bc10870454d00..67b6335a47065 100644 --- a/recipes/ucsc-bigwigsummary/build.sh +++ b/recipes/ucsc-bigwigsummary/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigSummary && make -j ${CPU_COUNT}) -cp bin/bigWigSummary "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigSummary" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigSummary && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigSummary "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigSummary" diff --git a/recipes/ucsc-bigwigsummary/include.patch b/recipes/ucsc-bigwigsummary/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigsummary/include.patch +++ b/recipes/ucsc-bigwigsummary/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml index ca2ca18d6646b..8b307b4221b64 100644 --- a/recipes/ucsc-bigwigsummary/meta.yaml +++ b/recipes/ucsc-bigwigsummary/meta.yaml @@ -1,54 +1,57 @@ {% set package = "ucsc-bigwigsummary" %} {% set program = "bigWigSummary" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage(package|lower, max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract summary information from a bigWig file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-bigwigtobedgraph/build.sh b/recipes/ucsc-bigwigtobedgraph/build.sh index 4d79a8a8afcb7..d9ee8a1c48c9c 100644 --- a/recipes/ucsc-bigwigtobedgraph/build.sh +++ b/recipes/ucsc-bigwigtobedgraph/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigToBedGraph && make -j ${CPU_COUNT}) -cp bin/bigWigToBedGraph "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigToBedGraph" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigToBedGraph && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigToBedGraph "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigToBedGraph" diff --git a/recipes/ucsc-bigwigtobedgraph/include.patch b/recipes/ucsc-bigwigtobedgraph/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigtobedgraph/include.patch +++ b/recipes/ucsc-bigwigtobedgraph/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigtobedgraph/meta.yaml b/recipes/ucsc-bigwigtobedgraph/meta.yaml index 03565119fb3c5..3cc5185b0c350 100644 --- a/recipes/ucsc-bigwigtobedgraph/meta.yaml +++ b/recipes/ucsc-bigwigtobedgraph/meta.yaml @@ -1,22 +1,21 @@ {% set package = "ucsc-bigwigtobedgraph" %} {% set program = "bigWigToBedGraph" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -24,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence + exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from bigWig to bedGraph format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-bigwigtowig/build.sh b/recipes/ucsc-bigwigtowig/build.sh index a437ceb086a47..a1977c231e86f 100644 --- a/recipes/ucsc-bigwigtowig/build.sh +++ b/recipes/ucsc-bigwigtowig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/bigWigToWig && make -j ${CPU_COUNT}) -cp bin/bigWigToWig "$PREFIX/bin" -chmod +x "$PREFIX/bin/bigWigToWig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/bigWigToWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/bigWigToWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/bigWigToWig" diff --git a/recipes/ucsc-bigwigtowig/include.patch b/recipes/ucsc-bigwigtowig/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-bigwigtowig/include.patch +++ b/recipes/ucsc-bigwigtowig/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-bigwigtowig/meta.yaml b/recipes/ucsc-bigwigtowig/meta.yaml index 31e4bcee47493..af93e4083efd4 100644 --- a/recipes/ucsc-bigwigtowig/meta.yaml +++ b/recipes/ucsc-bigwigtowig/meta.yaml @@ -1,54 +1,57 @@ {% set package = "ucsc-bigwigtowig" %} {% set program = "bigWigToWig" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage(package, max_pin="x") }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert bigWig to wig. This will keep more of the same structure of the original wig than bigWigToBedGraph does, but still will break up large stepped sections into smaller ones." + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert bigWig to wig. This will keep more of the same structure of the" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-blasttopsl/build.sh b/recipes/ucsc-blasttopsl/build.sh index 529365f0499e5..4e504991b1d17 100644 --- a/recipes/ucsc-blasttopsl/build.sh +++ b/recipes/ucsc-blasttopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/blastToPsl && make) -cp bin/blastToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/blastToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/blastToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/blastToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/blastToPsl" diff --git a/recipes/ucsc-blasttopsl/include.patch b/recipes/ucsc-blasttopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-blasttopsl/include.patch +++ b/recipes/ucsc-blasttopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-blasttopsl/meta.yaml b/recipes/ucsc-blasttopsl/meta.yaml index c50f577a4a6af..905368c1cacaa 100644 --- a/recipes/ucsc-blasttopsl/meta.yaml +++ b/recipes/ucsc-blasttopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-blasttopsl" %} {% set program = "blastToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert blast alignments to PSLs." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-blat/build.sh b/recipes/ucsc-blat/build.sh index 90db359833d44..abeab8ea7afd6 100644 --- a/recipes/ucsc-blat/build.sh +++ b/recipes/ucsc-blat/build.sh @@ -1,18 +1,21 @@ #!/bin/bash -export USE_HIC=0 + +set -xe + mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) -export BINDIR=`pwd`/bin +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p ${BINDIR} -(cd ${SRC_DIR}/kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd ${SRC_DIR}/kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd ${SRC_DIR}/kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd ${SRC_DIR}/kent/src/blat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f ${SRC_DIR}/bin/blat "${PREFIX}/bin" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/blat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/blat "${PREFIX}/bin" chmod 0755 "${PREFIX}/bin/blat" diff --git a/recipes/ucsc-blat/include.patch b/recipes/ucsc-blat/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-blat/include.patch +++ b/recipes/ucsc-blat/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-blat/meta.yaml b/recipes/ucsc-blat/meta.yaml index 089b3c02933a3..3a050f884b74b 100644 --- a/recipes/ucsc-blat/meta.yaml +++ b/recipes/ucsc-blat/meta.yaml @@ -1,38 +1,41 @@ {% set package = "ucsc-blat" %} {% set program = "blat" %} -{% set version = "468" %} -{% set sha256 = "f57b49be7e4eeb0719ac9414ca8878f93916fc3eb8dd408c8f7e076a999d1ca8" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch + - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-blat', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid + - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -41,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" - summary: "Standalone BLAT v. 39x1 fast sequence search command line tool" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Standalone BLAT v. 36x2 fast sequence search command line tool" dev_url: "https://github.com/ucscGenomeBrowser/kent" - doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/v{{ version }}_base/README" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-catdir/build.sh b/recipes/ucsc-catdir/build.sh index 615f2c28219a0..59b45dc68486c 100644 --- a/recipes/ucsc-catdir/build.sh +++ b/recipes/ucsc-catdir/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/catDir && make) -cp bin/catDir "$PREFIX/bin" -chmod +x "$PREFIX/bin/catDir" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/catDir && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/catDir "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/catDir" diff --git a/recipes/ucsc-catdir/include.patch b/recipes/ucsc-catdir/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-catdir/include.patch +++ b/recipes/ucsc-catdir/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-catdir/meta.yaml b/recipes/ucsc-catdir/meta.yaml index ec99f3e160dc9..9443ff4922d67 100644 --- a/recipes/ucsc-catdir/meta.yaml +++ b/recipes/ucsc-catdir/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-catdir" %} {% set program = "catDir" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "concatenate files in directory to stdout." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-catuncomment/build.sh b/recipes/ucsc-catuncomment/build.sh index e633331bb5d99..a6488e4ee3858 100644 --- a/recipes/ucsc-catuncomment/build.sh +++ b/recipes/ucsc-catuncomment/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/catUncomment && make) -cp bin/catUncomment "$PREFIX/bin" -chmod +x "$PREFIX/bin/catUncomment" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/catUncomment && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/catUncomment "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/catUncomment" diff --git a/recipes/ucsc-catuncomment/include.patch b/recipes/ucsc-catuncomment/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-catuncomment/include.patch +++ b/recipes/ucsc-catuncomment/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-catuncomment/meta.yaml b/recipes/ucsc-catuncomment/meta.yaml index 0eb80f7890c09..4e34d400fbd36 100644 --- a/recipes/ucsc-catuncomment/meta.yaml +++ b/recipes/ucsc-catuncomment/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-catuncomment" %} {% set program = "catUncomment" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Concatenate input removing lines that start with '#'" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainantirepeat/build.sh b/recipes/ucsc-chainantirepeat/build.sh index 4b96355a7cca0..42129d7ba0d38 100644 --- a/recipes/ucsc-chainantirepeat/build.sh +++ b/recipes/ucsc-chainantirepeat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainAntiRepeat && make) -cp bin/chainAntiRepeat "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainAntiRepeat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainAntiRepeat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainAntiRepeat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainAntiRepeat" diff --git a/recipes/ucsc-chainantirepeat/include.patch b/recipes/ucsc-chainantirepeat/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainantirepeat/include.patch +++ b/recipes/ucsc-chainantirepeat/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainantirepeat/meta.yaml b/recipes/ucsc-chainantirepeat/meta.yaml index c08a1b271ba4a..0ecd147dd4112 100644 --- a/recipes/ucsc-chainantirepeat/meta.yaml +++ b/recipes/ucsc-chainantirepeat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainantirepeat" %} {% set program = "chainAntiRepeat" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,28 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get rid of chains that are primarily the results of repeats and degenerate DNA" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainfilter/build.sh b/recipes/ucsc-chainfilter/build.sh index 6ed9ac45b5549..10d08403f1c62 100644 --- a/recipes/ucsc-chainfilter/build.sh +++ b/recipes/ucsc-chainfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainFilter && make) -cp bin/chainFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainFilter" diff --git a/recipes/ucsc-chainfilter/include.patch b/recipes/ucsc-chainfilter/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainfilter/include.patch +++ b/recipes/ucsc-chainfilter/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainfilter/meta.yaml b/recipes/ucsc-chainfilter/meta.yaml index eb41f55eb619f..950b6e95f0bba 100644 --- a/recipes/ucsc-chainfilter/meta.yaml +++ b/recipes/ucsc-chainfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainfilter" %} {% set program = "chainFilter" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,28 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter chain files. Output goes to standard out." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainmergesort/build.sh b/recipes/ucsc-chainmergesort/build.sh index afd3f10975fbc..d6577def526dc 100644 --- a/recipes/ucsc-chainmergesort/build.sh +++ b/recipes/ucsc-chainmergesort/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainMergeSort && make) -cp bin/chainMergeSort "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainMergeSort" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainMergeSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainMergeSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainMergeSort" diff --git a/recipes/ucsc-chainmergesort/include.patch b/recipes/ucsc-chainmergesort/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainmergesort/include.patch +++ b/recipes/ucsc-chainmergesort/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainmergesort/meta.yaml b/recipes/ucsc-chainmergesort/meta.yaml index a8116c2079423..ae45368e76907 100644 --- a/recipes/ucsc-chainmergesort/meta.yaml +++ b/recipes/ucsc-chainmergesort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainmergesort" %} {% set program = "chainMergeSort" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,28 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Combine sorted files into larger sorted file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainnet/build.sh b/recipes/ucsc-chainnet/build.sh index d374b876a973a..f90815a193a1d 100644 --- a/recipes/ucsc-chainnet/build.sh +++ b/recipes/ucsc-chainnet/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainNet && make) -cp bin/chainNet "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainNet" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainNet && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainNet "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainNet" diff --git a/recipes/ucsc-chainnet/include.patch b/recipes/ucsc-chainnet/include.patch index 5404b18b5467a..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainnet/include.patch +++ b/recipes/ucsc-chainnet/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif - + HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include - ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include + # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-chainnet/meta.yaml b/recipes/ucsc-chainnet/meta.yaml index 070f24c45a620..55b46b9d727b0 100644 --- a/recipes/ucsc-chainnet/meta.yaml +++ b/recipes/ucsc-chainnet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainnet" %} {% set program = "chainNet" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make alignment nets out of chains" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainprenet/build.sh b/recipes/ucsc-chainprenet/build.sh index 63ca58dde82ac..30c78ac9541a4 100644 --- a/recipes/ucsc-chainprenet/build.sh +++ b/recipes/ucsc-chainprenet/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainPreNet && make) -cp bin/chainPreNet "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainPreNet" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainPreNet && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainPreNet "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainPreNet" diff --git a/recipes/ucsc-chainprenet/include.patch b/recipes/ucsc-chainprenet/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainprenet/include.patch +++ b/recipes/ucsc-chainprenet/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainprenet/meta.yaml b/recipes/ucsc-chainprenet/meta.yaml index 748d450bbaa02..02c19c160aef0 100644 --- a/recipes/ucsc-chainprenet/meta.yaml +++ b/recipes/ucsc-chainprenet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainprenet" %} {% set program = "chainPreNet" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Remove chains that don't have a chance of being netted" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainsort/build.sh b/recipes/ucsc-chainsort/build.sh index aa1b99bc6019b..2ebbff9ed471a 100644 --- a/recipes/ucsc-chainsort/build.sh +++ b/recipes/ucsc-chainsort/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainSort && make) -cp bin/chainSort "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainSort" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainSort" diff --git a/recipes/ucsc-chainsort/include.patch b/recipes/ucsc-chainsort/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainsort/include.patch +++ b/recipes/ucsc-chainsort/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-chainsort/meta.yaml b/recipes/ucsc-chainsort/meta.yaml index 3864af0708530..93c9d98b79b37 100644 --- a/recipes/ucsc-chainsort/meta.yaml +++ b/recipes/ucsc-chainsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainsort" %} {% set program = "chainSort" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -17,34 +17,41 @@ build: skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage("ucsc-chainsort", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Sort chains. By default sorts by score." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainsplit/build.sh b/recipes/ucsc-chainsplit/build.sh index 904b5af20b961..86485b0bf816f 100644 --- a/recipes/ucsc-chainsplit/build.sh +++ b/recipes/ucsc-chainsplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainSplit && make) -cp bin/chainSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainSplit" diff --git a/recipes/ucsc-chainsplit/include.patch b/recipes/ucsc-chainsplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainsplit/include.patch +++ b/recipes/ucsc-chainsplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainsplit/meta.yaml b/recipes/ucsc-chainsplit/meta.yaml index 879198f6e1dc9..8904f36ce5819 100644 --- a/recipes/ucsc-chainsplit/meta.yaml +++ b/recipes/ucsc-chainsplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainsplit" %} {% set program = "chainSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split chains up by target or query sequence" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainstitchid/build.sh b/recipes/ucsc-chainstitchid/build.sh index 5a737a5c85003..10dfddf7ed04e 100644 --- a/recipes/ucsc-chainstitchid/build.sh +++ b/recipes/ucsc-chainstitchid/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainStitchId && make) -cp bin/chainStitchId "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainStitchId" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainStitchId && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainStitchId "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainStitchId" diff --git a/recipes/ucsc-chainstitchid/include.patch b/recipes/ucsc-chainstitchid/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainstitchid/include.patch +++ b/recipes/ucsc-chainstitchid/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainstitchid/meta.yaml b/recipes/ucsc-chainstitchid/meta.yaml index 2001b5df994a4..ef2cfd4aeacd6 100644 --- a/recipes/ucsc-chainstitchid/meta.yaml +++ b/recipes/ucsc-chainstitchid/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainstitchid" %} {% set program = "chainStitchId" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Join chain fragments with the same chain ID into a single" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chainswap/build.sh b/recipes/ucsc-chainswap/build.sh index 361d0fad14946..8eb218a29a95a 100644 --- a/recipes/ucsc-chainswap/build.sh +++ b/recipes/ucsc-chainswap/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainSwap && make) -cp bin/chainSwap "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainSwap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainSwap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainSwap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainSwap" diff --git a/recipes/ucsc-chainswap/include.patch b/recipes/ucsc-chainswap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chainswap/include.patch +++ b/recipes/ucsc-chainswap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chainswap/meta.yaml b/recipes/ucsc-chainswap/meta.yaml index a4781ec42be5d..4e91525fb6b79 100644 --- a/recipes/ucsc-chainswap/meta.yaml +++ b/recipes/ucsc-chainswap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chainswap" %} {% set program = "chainSwap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Swap target and query in chain" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chaintoaxt/build.sh b/recipes/ucsc-chaintoaxt/build.sh index 183b350517e6a..04441646d7916 100644 --- a/recipes/ucsc-chaintoaxt/build.sh +++ b/recipes/ucsc-chaintoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainToAxt && make) -cp bin/chainToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainToAxt" diff --git a/recipes/ucsc-chaintoaxt/include.patch b/recipes/ucsc-chaintoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chaintoaxt/include.patch +++ b/recipes/ucsc-chaintoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chaintoaxt/meta.yaml b/recipes/ucsc-chaintoaxt/meta.yaml index b9c5445fd18b2..77d4ae748c889 100644 --- a/recipes/ucsc-chaintoaxt/meta.yaml +++ b/recipes/ucsc-chaintoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chaintoaxt" %} {% set program = "chainToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from chain to axt file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chaintopsl/build.sh b/recipes/ucsc-chaintopsl/build.sh index 73cc58fd9a243..744cad97874af 100644 --- a/recipes/ucsc-chaintopsl/build.sh +++ b/recipes/ucsc-chaintopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainToPsl && make) -cp bin/chainToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainToPsl" diff --git a/recipes/ucsc-chaintopsl/include.patch b/recipes/ucsc-chaintopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chaintopsl/include.patch +++ b/recipes/ucsc-chaintopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chaintopsl/meta.yaml b/recipes/ucsc-chaintopsl/meta.yaml index 0bc996af09ba1..ced6ca5ebea90 100644 --- a/recipes/ucsc-chaintopsl/meta.yaml +++ b/recipes/ucsc-chaintopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chaintopsl" %} {% set program = "chainToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert chain file to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chaintopslbasic/build.sh b/recipes/ucsc-chaintopslbasic/build.sh index 0c1f25b1e30dc..4f3b66b44fedb 100644 --- a/recipes/ucsc-chaintopslbasic/build.sh +++ b/recipes/ucsc-chaintopslbasic/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/chainToPslBasic && make) -cp bin/chainToPslBasic "$PREFIX/bin" -chmod +x "$PREFIX/bin/chainToPslBasic" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/chainToPslBasic && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chainToPslBasic "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chainToPslBasic" diff --git a/recipes/ucsc-chaintopslbasic/include.patch b/recipes/ucsc-chaintopslbasic/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chaintopslbasic/include.patch +++ b/recipes/ucsc-chaintopslbasic/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chaintopslbasic/meta.yaml b/recipes/ucsc-chaintopslbasic/meta.yaml index fba9f93d81f94..9a9683eff74f7 100644 --- a/recipes/ucsc-chaintopslbasic/meta.yaml +++ b/recipes/ucsc-chaintopslbasic/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chaintopslbasic" %} {% set program = "chainToPslBasic" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Basic conversion chain file to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checkagpandfa/build.sh b/recipes/ucsc-checkagpandfa/build.sh index 73ca488d61f8f..ad3b4d10ece14 100644 --- a/recipes/ucsc-checkagpandfa/build.sh +++ b/recipes/ucsc-checkagpandfa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/gigAssembler/checkAgpAndFa && make) -cp bin/checkAgpAndFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkAgpAndFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/gigAssembler/checkAgpAndFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkAgpAndFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkAgpAndFa" diff --git a/recipes/ucsc-checkagpandfa/include.patch b/recipes/ucsc-checkagpandfa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checkagpandfa/include.patch +++ b/recipes/ucsc-checkagpandfa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checkagpandfa/meta.yaml b/recipes/ucsc-checkagpandfa/meta.yaml index 602c1b2589e17..5a739b8c2d0db 100644 --- a/recipes/ucsc-checkagpandfa/meta.yaml +++ b/recipes/ucsc-checkagpandfa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checkagpandfa" %} {% set program = "checkAgpAndFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "takes a .agp file and .fa file and ensures that they are in synch" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checkcoveragegaps/build.sh b/recipes/ucsc-checkcoveragegaps/build.sh index ef5ebe0df0a02..eb941d1941048 100644 --- a/recipes/ucsc-checkcoveragegaps/build.sh +++ b/recipes/ucsc-checkcoveragegaps/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/checkCoverageGaps && make) -cp bin/checkCoverageGaps "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkCoverageGaps" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/checkCoverageGaps && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkCoverageGaps "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkCoverageGaps" diff --git a/recipes/ucsc-checkcoveragegaps/include.patch b/recipes/ucsc-checkcoveragegaps/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checkcoveragegaps/include.patch +++ b/recipes/ucsc-checkcoveragegaps/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checkcoveragegaps/meta.yaml b/recipes/ucsc-checkcoveragegaps/meta.yaml index b3d0db6ae4843..f3760515616c3 100644 --- a/recipes/ucsc-checkcoveragegaps/meta.yaml +++ b/recipes/ucsc-checkcoveragegaps/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checkcoveragegaps" %} {% set program = "checkCoverageGaps" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Check for biggest gap in coverage for a list of tracks." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checkhgfindspec/build.sh b/recipes/ucsc-checkhgfindspec/build.sh index c89af8112bd23..a1d8fa895c2af 100644 --- a/recipes/ucsc-checkhgfindspec/build.sh +++ b/recipes/ucsc-checkhgfindspec/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/checkHgFindSpec && make) -cp bin/checkHgFindSpec "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkHgFindSpec" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/checkHgFindSpec && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkHgFindSpec "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkHgFindSpec" diff --git a/recipes/ucsc-checkhgfindspec/include.patch b/recipes/ucsc-checkhgfindspec/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checkhgfindspec/include.patch +++ b/recipes/ucsc-checkhgfindspec/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checkhgfindspec/meta.yaml b/recipes/ucsc-checkhgfindspec/meta.yaml index 7d0c1b14e7bda..344ee0e75f466 100644 --- a/recipes/ucsc-checkhgfindspec/meta.yaml +++ b/recipes/ucsc-checkhgfindspec/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checkhgfindspec" %} {% set program = "checkHgFindSpec" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "test and describe search specs in hgFindSpec tables." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-checktablecoords/build.sh b/recipes/ucsc-checktablecoords/build.sh index 32521004ac2cd..91bb2e088ce06 100644 --- a/recipes/ucsc-checktablecoords/build.sh +++ b/recipes/ucsc-checktablecoords/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/checkTableCoords && make) -cp bin/checkTableCoords "$PREFIX/bin" -chmod +x "$PREFIX/bin/checkTableCoords" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/checkTableCoords && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/checkTableCoords "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/checkTableCoords" diff --git a/recipes/ucsc-checktablecoords/include.patch b/recipes/ucsc-checktablecoords/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-checktablecoords/include.patch +++ b/recipes/ucsc-checktablecoords/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-checktablecoords/meta.yaml b/recipes/ucsc-checktablecoords/meta.yaml index 791004d8305d7..5debd1bc64c66 100644 --- a/recipes/ucsc-checktablecoords/meta.yaml +++ b/recipes/ucsc-checktablecoords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-checktablecoords" %} {% set program = "checkTableCoords" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "check invariants on genomic coords in table(s)." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chopfalines/build.sh b/recipes/ucsc-chopfalines/build.sh index ee55545a7dfb8..a58ab6b37ac2a 100644 --- a/recipes/ucsc-chopfalines/build.sh +++ b/recipes/ucsc-chopfalines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/chopFaLines && make) -cp bin/chopFaLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/chopFaLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/chopFaLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chopFaLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chopFaLines" diff --git a/recipes/ucsc-chopfalines/include.patch b/recipes/ucsc-chopfalines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chopfalines/include.patch +++ b/recipes/ucsc-chopfalines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chopfalines/meta.yaml b/recipes/ucsc-chopfalines/meta.yaml index 82f95f1e65f16..55a8833c00e82 100644 --- a/recipes/ucsc-chopfalines/meta.yaml +++ b/recipes/ucsc-chopfalines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chopfalines" %} {% set program = "chopFaLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Read in FA file with long lines and rewrite it with shorter lines" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chromgraphfrombin/build.sh b/recipes/ucsc-chromgraphfrombin/build.sh index f4e4f1cd6a5c7..abe23d1d58239 100644 --- a/recipes/ucsc-chromgraphfrombin/build.sh +++ b/recipes/ucsc-chromgraphfrombin/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/chromGraphFromBin && make) -cp bin/chromGraphFromBin "$PREFIX/bin" -chmod +x "$PREFIX/bin/chromGraphFromBin" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/chromGraphFromBin && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chromGraphFromBin "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chromGraphFromBin" diff --git a/recipes/ucsc-chromgraphfrombin/include.patch b/recipes/ucsc-chromgraphfrombin/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chromgraphfrombin/include.patch +++ b/recipes/ucsc-chromgraphfrombin/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chromgraphfrombin/meta.yaml b/recipes/ucsc-chromgraphfrombin/meta.yaml index d5fee658365da..346ea09a30bca 100644 --- a/recipes/ucsc-chromgraphfrombin/meta.yaml +++ b/recipes/ucsc-chromgraphfrombin/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chromgraphfrombin" %} {% set program = "chromGraphFromBin" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert chromGraph binary to ascii format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-chromgraphtobin/build.sh b/recipes/ucsc-chromgraphtobin/build.sh index 3cfddf7a01494..e48eda9b05ff5 100644 --- a/recipes/ucsc-chromgraphtobin/build.sh +++ b/recipes/ucsc-chromgraphtobin/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/chromGraphToBin && make) -cp bin/chromGraphToBin "$PREFIX/bin" -chmod +x "$PREFIX/bin/chromGraphToBin" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/chromGraphToBin && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/chromGraphToBin "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/chromGraphToBin" diff --git a/recipes/ucsc-chromgraphtobin/include.patch b/recipes/ucsc-chromgraphtobin/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-chromgraphtobin/include.patch +++ b/recipes/ucsc-chromgraphtobin/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-chromgraphtobin/meta.yaml b/recipes/ucsc-chromgraphtobin/meta.yaml index 3e585a0142a8f..84176419d5b18 100644 --- a/recipes/ucsc-chromgraphtobin/meta.yaml +++ b/recipes/ucsc-chromgraphtobin/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-chromgraphtobin" %} {% set program = "chromGraphToBin" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make binary version of chromGraph." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-coltransform/build.sh b/recipes/ucsc-coltransform/build.sh index a98809f9c583c..17f4d40047c93 100644 --- a/recipes/ucsc-coltransform/build.sh +++ b/recipes/ucsc-coltransform/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/colTransform && make) -cp bin/colTransform "$PREFIX/bin" -chmod +x "$PREFIX/bin/colTransform" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/colTransform && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/colTransform "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/colTransform" diff --git a/recipes/ucsc-coltransform/include.patch b/recipes/ucsc-coltransform/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-coltransform/include.patch +++ b/recipes/ucsc-coltransform/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-coltransform/meta.yaml b/recipes/ucsc-coltransform/meta.yaml index 8db80ad0ad41b..46a6ce6c314fa 100644 --- a/recipes/ucsc-coltransform/meta.yaml +++ b/recipes/ucsc-coltransform/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-coltransform" %} {% set program = "colTransform" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add and/or multiply column by constant." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-countchars/build.sh b/recipes/ucsc-countchars/build.sh index e2c225cd7ebe3..ab3cb84cb1983 100644 --- a/recipes/ucsc-countchars/build.sh +++ b/recipes/ucsc-countchars/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/countChars && make) -cp bin/countChars "$PREFIX/bin" -chmod +x "$PREFIX/bin/countChars" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/countChars && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/countChars "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/countChars" diff --git a/recipes/ucsc-countchars/include.patch b/recipes/ucsc-countchars/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-countchars/include.patch +++ b/recipes/ucsc-countchars/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-countchars/meta.yaml b/recipes/ucsc-countchars/meta.yaml index a5edbbf355e7d..3191991de187e 100644 --- a/recipes/ucsc-countchars/meta.yaml +++ b/recipes/ucsc-countchars/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-countchars" %} {% set program = "countChars" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Count the number of occurrences of a particular char" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-crtreeindexbed/build.sh b/recipes/ucsc-crtreeindexbed/build.sh index a5c31fd2e8f40..32c54dab05cde 100644 --- a/recipes/ucsc-crtreeindexbed/build.sh +++ b/recipes/ucsc-crtreeindexbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/crTreeIndexBed && make) -cp bin/crTreeIndexBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/crTreeIndexBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/crTreeIndexBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/crTreeIndexBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/crTreeIndexBed" diff --git a/recipes/ucsc-crtreeindexbed/include.patch b/recipes/ucsc-crtreeindexbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-crtreeindexbed/include.patch +++ b/recipes/ucsc-crtreeindexbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-crtreeindexbed/meta.yaml b/recipes/ucsc-crtreeindexbed/meta.yaml index b27fbf72f00c6..59945d6280836 100644 --- a/recipes/ucsc-crtreeindexbed/meta.yaml +++ b/recipes/ucsc-crtreeindexbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-crtreeindexbed" %} {% set program = "crTreeIndexBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create an index for a bed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-crtreesearchbed/build.sh b/recipes/ucsc-crtreesearchbed/build.sh index a12dde560da6c..3ff4031d4a04a 100644 --- a/recipes/ucsc-crtreesearchbed/build.sh +++ b/recipes/ucsc-crtreesearchbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/crTreeSearchBed && make) -cp bin/crTreeSearchBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/crTreeSearchBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/crTreeSearchBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/crTreeSearchBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/crTreeSearchBed" diff --git a/recipes/ucsc-crtreesearchbed/include.patch b/recipes/ucsc-crtreesearchbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-crtreesearchbed/include.patch +++ b/recipes/ucsc-crtreesearchbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-crtreesearchbed/meta.yaml b/recipes/ucsc-crtreesearchbed/meta.yaml index 2066d7d3f5600..cf88771bb980d 100644 --- a/recipes/ucsc-crtreesearchbed/meta.yaml +++ b/recipes/ucsc-crtreesearchbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-crtreesearchbed" %} {% set program = "crTreeSearchBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Search a crTree indexed bed file and print all items that overlap query." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-dbsnoop/build.sh b/recipes/ucsc-dbsnoop/build.sh index 262a37a241c74..aa3011731bccf 100644 --- a/recipes/ucsc-dbsnoop/build.sh +++ b/recipes/ucsc-dbsnoop/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/schema/dbSnoop && make) -cp bin/dbSnoop "$PREFIX/bin" -chmod +x "$PREFIX/bin/dbSnoop" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/schema/dbSnoop && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/dbSnoop "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/dbSnoop" diff --git a/recipes/ucsc-dbsnoop/include.patch b/recipes/ucsc-dbsnoop/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-dbsnoop/include.patch +++ b/recipes/ucsc-dbsnoop/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-dbsnoop/meta.yaml b/recipes/ucsc-dbsnoop/meta.yaml index e72dffb9fd650..b20c4a5c34f80 100644 --- a/recipes/ucsc-dbsnoop/meta.yaml +++ b/recipes/ucsc-dbsnoop/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-dbsnoop" %} {% set program = "dbSnoop" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Produce an overview of a database." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-dbtrash/build.sh b/recipes/ucsc-dbtrash/build.sh index 486a57847c65e..9052d214175ac 100644 --- a/recipes/ucsc-dbtrash/build.sh +++ b/recipes/ucsc-dbtrash/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/dbTrash && make) -cp bin/dbTrash "$PREFIX/bin" -chmod +x "$PREFIX/bin/dbTrash" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/dbTrash && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/dbTrash "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/dbTrash" diff --git a/recipes/ucsc-dbtrash/include.patch b/recipes/ucsc-dbtrash/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-dbtrash/include.patch +++ b/recipes/ucsc-dbtrash/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-dbtrash/meta.yaml b/recipes/ucsc-dbtrash/meta.yaml index 66ad1fd75c48d..9a1fe0aa70b76 100644 --- a/recipes/ucsc-dbtrash/meta.yaml +++ b/recipes/ucsc-dbtrash/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-dbtrash" %} {% set program = "dbTrash" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "drop tables from a database older than specified N hours" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-estorient/build.sh b/recipes/ucsc-estorient/build.sh index 5566c5e5ad866..d7641fd6d458b 100644 --- a/recipes/ucsc-estorient/build.sh +++ b/recipes/ucsc-estorient/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/estOrient && make) -cp bin/estOrient "$PREFIX/bin" -chmod +x "$PREFIX/bin/estOrient" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/estOrient && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/estOrient "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/estOrient" diff --git a/recipes/ucsc-estorient/include.patch b/recipes/ucsc-estorient/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-estorient/include.patch +++ b/recipes/ucsc-estorient/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-estorient/meta.yaml b/recipes/ucsc-estorient/meta.yaml index 9d1af8682029d..52c9e91f81aa5 100644 --- a/recipes/ucsc-estorient/meta.yaml +++ b/recipes/ucsc-estorient/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-estorient" %} {% set program = "estOrient" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,27 +27,36 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Read ESTs from a database and determine orientation based on estOrientInfo table or direction in gbCdnaInfo table. Update PSLs so that the strand reflects the direction of transcription. By default, PSLs where the direction can't be determined are dropped. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-expmatrixtobarchartbed/build.sh b/recipes/ucsc-expmatrixtobarchartbed/build.sh index 1a0f89d979c8a..4d969ac373b84 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/build.sh +++ b/recipes/ucsc-expmatrixtobarchartbed/build.sh @@ -1,4 +1,7 @@ #!/bin/bash + +set -xe + mkdir -p "$PREFIX/bin" -cp kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/expMatrixToBarchartBed" +cp kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/expMatrixToBarchartBed" diff --git a/recipes/ucsc-expmatrixtobarchartbed/include.patch b/recipes/ucsc-expmatrixtobarchartbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/include.patch +++ b/recipes/ucsc-expmatrixtobarchartbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml index d553009fe4404..c3733642eab60 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml +++ b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml @@ -1,30 +1,39 @@ {% set package = "ucsc-expmatrixtobarchartbed" %} {% set program = "expMatrixToBarchartBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" version: "{{ version }}" source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{ version }.src.tgz" sha256: "{{ sha256 }}" patches: - "include.patch" build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - { pin_subpackage(package, max_pin=None) } requirements: build: + - {{ compiler('c') }} host: + - libpng + - libuuid + - mysql-connector-c + - libopenssl-static + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -40,3 +49,12 @@ about: Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-faalign/build.sh b/recipes/ucsc-faalign/build.sh index a2075d4dccc91..ab0abc9c5a13a 100644 --- a/recipes/ucsc-faalign/build.sh +++ b/recipes/ucsc-faalign/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faAlign && make) -cp bin/faAlign "$PREFIX/bin" -chmod +x "$PREFIX/bin/faAlign" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faAlign && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faAlign "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faAlign" diff --git a/recipes/ucsc-faalign/include.patch b/recipes/ucsc-faalign/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-faalign/include.patch +++ b/recipes/ucsc-faalign/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-faalign/meta.yaml b/recipes/ucsc-faalign/meta.yaml index bce04cc6ed964..e5bb10fb1e460 100644 --- a/recipes/ucsc-faalign/meta.yaml +++ b/recipes/ucsc-faalign/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-faalign" %} {% set program = "faAlign" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Align two fasta files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-facmp/build.sh b/recipes/ucsc-facmp/build.sh index 63045c9a3e2b8..a5d4d479e44b0 100644 --- a/recipes/ucsc-facmp/build.sh +++ b/recipes/ucsc-facmp/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faCmp && make) -cp bin/faCmp "$PREFIX/bin" -chmod +x "$PREFIX/bin/faCmp" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faCmp && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faCmp "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faCmp" diff --git a/recipes/ucsc-facmp/include.patch b/recipes/ucsc-facmp/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-facmp/include.patch +++ b/recipes/ucsc-facmp/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-facmp/meta.yaml b/recipes/ucsc-facmp/meta.yaml index c418a4cb1aea9..7a45c7f7ff32d 100644 --- a/recipes/ucsc-facmp/meta.yaml +++ b/recipes/ucsc-facmp/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-facmp" %} {% set program = "faCmp" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Compare two .fa files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-facount/build.sh b/recipes/ucsc-facount/build.sh index 728b733768684..3c2c36f703f08 100644 --- a/recipes/ucsc-facount/build.sh +++ b/recipes/ucsc-facount/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faCount && make) -cp bin/faCount "$PREFIX/bin" -chmod +x "$PREFIX/bin/faCount" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faCount && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faCount "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faCount" diff --git a/recipes/ucsc-facount/include.patch b/recipes/ucsc-facount/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-facount/include.patch +++ b/recipes/ucsc-facount/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-facount/meta.yaml b/recipes/ucsc-facount/meta.yaml index cdadf370f0701..e09912d257d02 100644 --- a/recipes/ucsc-facount/meta.yaml +++ b/recipes/ucsc-facount/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-facount" %} {% set program = "faCount" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "count base statistics and CpGs in FA files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fafilter/build.sh b/recipes/ucsc-fafilter/build.sh index 35517aac7e251..967758179cadb 100644 --- a/recipes/ucsc-fafilter/build.sh +++ b/recipes/ucsc-fafilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faFilter && make) -cp bin/faFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/faFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faFilter" diff --git a/recipes/ucsc-fafilter/include.patch b/recipes/ucsc-fafilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fafilter/include.patch +++ b/recipes/ucsc-fafilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fafilter/meta.yaml b/recipes/ucsc-fafilter/meta.yaml index de8020cd7496a..ee67056366443 100644 --- a/recipes/ucsc-fafilter/meta.yaml +++ b/recipes/ucsc-fafilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fafilter" %} {% set program = "faFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter fa records, selecting ones that match the specified conditions" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fafiltern/build.sh b/recipes/ucsc-fafiltern/build.sh index 772564ca3074e..e7a910bc26cad 100644 --- a/recipes/ucsc-fafiltern/build.sh +++ b/recipes/ucsc-fafiltern/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faFilterN && make) -cp bin/faFilterN "$PREFIX/bin" -chmod +x "$PREFIX/bin/faFilterN" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faFilterN && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faFilterN "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faFilterN" diff --git a/recipes/ucsc-fafiltern/include.patch b/recipes/ucsc-fafiltern/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fafiltern/include.patch +++ b/recipes/ucsc-fafiltern/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fafiltern/meta.yaml b/recipes/ucsc-fafiltern/meta.yaml index d6d0f1112e23a..64f3693d3df25 100644 --- a/recipes/ucsc-fafiltern/meta.yaml +++ b/recipes/ucsc-fafiltern/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fafiltern" %} {% set program = "faFilterN" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get rid of sequences with too many N's" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fafrag/build.sh b/recipes/ucsc-fafrag/build.sh index cc8217d202654..bbde61befd833 100644 --- a/recipes/ucsc-fafrag/build.sh +++ b/recipes/ucsc-fafrag/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faFrag && make) -cp bin/faFrag "$PREFIX/bin" -chmod +x "$PREFIX/bin/faFrag" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faFrag && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faFrag "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faFrag" diff --git a/recipes/ucsc-fafrag/include.patch b/recipes/ucsc-fafrag/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fafrag/include.patch +++ b/recipes/ucsc-fafrag/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fafrag/meta.yaml b/recipes/ucsc-fafrag/meta.yaml index 74dbeee693c2e..63fbd2a2bc5cf 100644 --- a/recipes/ucsc-fafrag/meta.yaml +++ b/recipes/ucsc-fafrag/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fafrag" %} {% set program = "faFrag" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract a piece of DNA from a .fa file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fanoise/build.sh b/recipes/ucsc-fanoise/build.sh index 2c1848ec9a9dc..4b96dc8e7a9ad 100644 --- a/recipes/ucsc-fanoise/build.sh +++ b/recipes/ucsc-fanoise/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faNoise && make) -cp bin/faNoise "$PREFIX/bin" -chmod +x "$PREFIX/bin/faNoise" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faNoise && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faNoise "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faNoise" diff --git a/recipes/ucsc-fanoise/include.patch b/recipes/ucsc-fanoise/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fanoise/include.patch +++ b/recipes/ucsc-fanoise/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fanoise/meta.yaml b/recipes/ucsc-fanoise/meta.yaml index a89d4b85524be..6ba0418b05532 100644 --- a/recipes/ucsc-fanoise/meta.yaml +++ b/recipes/ucsc-fanoise/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fanoise" %} {% set program = "faNoise" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add noise to .fa file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-faonerecord/build.sh b/recipes/ucsc-faonerecord/build.sh index d2a4c53e9f283..af644537f494a 100644 --- a/recipes/ucsc-faonerecord/build.sh +++ b/recipes/ucsc-faonerecord/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faOneRecord && make) -cp bin/faOneRecord "$PREFIX/bin" -chmod +x "$PREFIX/bin/faOneRecord" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faOneRecord && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faOneRecord "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faOneRecord" diff --git a/recipes/ucsc-faonerecord/include.patch b/recipes/ucsc-faonerecord/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-faonerecord/include.patch +++ b/recipes/ucsc-faonerecord/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-faonerecord/meta.yaml b/recipes/ucsc-faonerecord/meta.yaml index 761f7d83bdc1a..d52e42e40b317 100644 --- a/recipes/ucsc-faonerecord/meta.yaml +++ b/recipes/ucsc-faonerecord/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-faonerecord" %} {% set program = "faOneRecord" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract a single record from a .FA file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fapolyasizes/build.sh b/recipes/ucsc-fapolyasizes/build.sh index 2a7659a5c4a58..383f0fdc8416b 100644 --- a/recipes/ucsc-fapolyasizes/build.sh +++ b/recipes/ucsc-fapolyasizes/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faPolyASizes && make) -cp bin/faPolyASizes "$PREFIX/bin" -chmod +x "$PREFIX/bin/faPolyASizes" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faPolyASizes && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faPolyASizes "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faPolyASizes" diff --git a/recipes/ucsc-fapolyasizes/include.patch b/recipes/ucsc-fapolyasizes/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fapolyasizes/include.patch +++ b/recipes/ucsc-fapolyasizes/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fapolyasizes/meta.yaml b/recipes/ucsc-fapolyasizes/meta.yaml index 55df8ed83732c..6dac4793b6b2e 100644 --- a/recipes/ucsc-fapolyasizes/meta.yaml +++ b/recipes/ucsc-fapolyasizes/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fapolyasizes" %} {% set program = "faPolyASizes" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get poly A sizes" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-farandomize/build.sh b/recipes/ucsc-farandomize/build.sh index 10bcbaa61dec2..992f3baa9537f 100644 --- a/recipes/ucsc-farandomize/build.sh +++ b/recipes/ucsc-farandomize/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faRandomize && make) -cp bin/faRandomize "$PREFIX/bin" -chmod +x "$PREFIX/bin/faRandomize" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faRandomize && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faRandomize "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faRandomize" diff --git a/recipes/ucsc-farandomize/include.patch b/recipes/ucsc-farandomize/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-farandomize/include.patch +++ b/recipes/ucsc-farandomize/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-farandomize/meta.yaml b/recipes/ucsc-farandomize/meta.yaml index 400b9d8b2578e..7a357380b6102 100644 --- a/recipes/ucsc-farandomize/meta.yaml +++ b/recipes/ucsc-farandomize/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-farandomize" %} {% set program = "faRandomize" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Program to create random fasta records" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-farc/build.sh b/recipes/ucsc-farc/build.sh index d68de0a45c997..5efc3188c34d8 100644 --- a/recipes/ucsc-farc/build.sh +++ b/recipes/ucsc-farc/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faRc && make) -cp bin/faRc "$PREFIX/bin" -chmod +x "$PREFIX/bin/faRc" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faRc && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faRc "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faRc" diff --git a/recipes/ucsc-farc/include.patch b/recipes/ucsc-farc/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-farc/include.patch +++ b/recipes/ucsc-farc/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-farc/meta.yaml b/recipes/ucsc-farc/meta.yaml index 544410aef81d7..59ad4f779fb2c 100644 --- a/recipes/ucsc-farc/meta.yaml +++ b/recipes/ucsc-farc/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-farc" %} {% set program = "faRc" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Reverse complement a FA file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fasize/build.sh b/recipes/ucsc-fasize/build.sh index 08610aaa04451..42e777e285924 100644 --- a/recipes/ucsc-fasize/build.sh +++ b/recipes/ucsc-fasize/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faSize && make) -cp bin/faSize "$PREFIX/bin" -chmod +x "$PREFIX/bin/faSize" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faSize && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faSize "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faSize" diff --git a/recipes/ucsc-fasize/include.patch b/recipes/ucsc-fasize/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fasize/include.patch +++ b/recipes/ucsc-fasize/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fasize/meta.yaml b/recipes/ucsc-fasize/meta.yaml index 295546709d3a1..e5ca815518a66 100644 --- a/recipes/ucsc-fasize/meta.yaml +++ b/recipes/ucsc-fasize/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasize" %} {% set program = "faSize" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "print total base count in fa files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fasomerecords/build.sh b/recipes/ucsc-fasomerecords/build.sh index b61bf19685404..94dda243aec45 100644 --- a/recipes/ucsc-fasomerecords/build.sh +++ b/recipes/ucsc-fasomerecords/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faSomeRecords && make) -cp bin/faSomeRecords "$PREFIX/bin" -chmod +x "$PREFIX/bin/faSomeRecords" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faSomeRecords && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faSomeRecords "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faSomeRecords" diff --git a/recipes/ucsc-fasomerecords/include.patch b/recipes/ucsc-fasomerecords/include.patch index e4831ef2dea13..edc04d0dc2f64 100644 --- a/recipes/ucsc-fasomerecords/include.patch +++ b/recipes/ucsc-fasomerecords/include.patch @@ -1,22 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ @@ -25,16 +25,3 @@ # expMatrixToBarchartBed """ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates. ---- kent/src/hg/lib/straw/makefile -+++ kent/src/hg/lib/straw/makefile -@@ -3,8 +3,8 @@ - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o - straw.o: straw.cpp straw.h -- ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -+ ${CXX} straw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o straw.o -I ${PREFIX}/include - cStraw.o: cStraw.cpp straw.h -- ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -+ ${CXX} cStraw.cpp ${KENT_INC} -g -c -lz -std=c++11 -lcurl -o cStraw.o -I ${PREFIX}/include - clean: - rm -f straw.o cStraw.o ../straw.o diff --git a/recipes/ucsc-fasomerecords/meta.yaml b/recipes/ucsc-fasomerecords/meta.yaml index 507bf2b0b7cd6..86fe4dda5cbc4 100644 --- a/recipes/ucsc-fasomerecords/meta.yaml +++ b/recipes/ucsc-fasomerecords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasomerecords" %} {% set program = "faSomeRecords" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -23,27 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - binutils >=2.32 # https://wiki.gentoo.org/wiki/Project:Toolchain/Binutils_2.32_upgrade_notes/elfutils_0.175:_unable_to_initialize_decompress_status_for_section_.debug_info - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract multiple fa records" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fasplit/build.sh b/recipes/ucsc-fasplit/build.sh index bf837fd78a605..ed7f37ba92c85 100644 --- a/recipes/ucsc-fasplit/build.sh +++ b/recipes/ucsc-fasplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faSplit && make) -cp bin/faSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/faSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faSplit" diff --git a/recipes/ucsc-fasplit/include.patch b/recipes/ucsc-fasplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fasplit/include.patch +++ b/recipes/ucsc-fasplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fasplit/meta.yaml b/recipes/ucsc-fasplit/meta.yaml index 1758efe8fe7d9..9b811fc0a565c 100644 --- a/recipes/ucsc-fasplit/meta.yaml +++ b/recipes/ucsc-fasplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fasplit" %} {% set program = "faSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split an fa file into several files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fastqstatsandsubsample/build.sh b/recipes/ucsc-fastqstatsandsubsample/build.sh index a06ee6dcb3901..56efb5ed3f796 100644 --- a/recipes/ucsc-fastqstatsandsubsample/build.sh +++ b/recipes/ucsc-fastqstatsandsubsample/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/fastqStatsAndSubsample && make) -cp bin/fastqStatsAndSubsample "$PREFIX/bin" -chmod +x "$PREFIX/bin/fastqStatsAndSubsample" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/fastqStatsAndSubsample && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/fastqStatsAndSubsample "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/fastqStatsAndSubsample" diff --git a/recipes/ucsc-fastqstatsandsubsample/include.patch b/recipes/ucsc-fastqstatsandsubsample/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fastqstatsandsubsample/include.patch +++ b/recipes/ucsc-fastqstatsandsubsample/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fastqstatsandsubsample/meta.yaml b/recipes/ucsc-fastqstatsandsubsample/meta.yaml index fa874a86c6770..ccdb6bfc69d23 100644 --- a/recipes/ucsc-fastqstatsandsubsample/meta.yaml +++ b/recipes/ucsc-fastqstatsandsubsample/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fastqstatsandsubsample" %} {% set program = "fastqStatsAndSubsample" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Go through a fastq file doing sanity checks and collecting stats" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fastqtofa/build.sh b/recipes/ucsc-fastqtofa/build.sh index a0eb7afc81495..0d73cb307256b 100644 --- a/recipes/ucsc-fastqtofa/build.sh +++ b/recipes/ucsc-fastqtofa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/fastqToFa && make) -cp bin/fastqToFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/fastqToFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/fastqToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/fastqToFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/fastqToFa" diff --git a/recipes/ucsc-fastqtofa/include.patch b/recipes/ucsc-fastqtofa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fastqtofa/include.patch +++ b/recipes/ucsc-fastqtofa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fastqtofa/meta.yaml b/recipes/ucsc-fastqtofa/meta.yaml index d2bcf5a600ff4..5bc623ded2330 100644 --- a/recipes/ucsc-fastqtofa/meta.yaml +++ b/recipes/ucsc-fastqtofa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fastqtofa" %} {% set program = "fastqToFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from fastq to fasta format." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fatofastq/build.sh b/recipes/ucsc-fatofastq/build.sh index 69dd94f808370..821b6b535ce86 100644 --- a/recipes/ucsc-fatofastq/build.sh +++ b/recipes/ucsc-fatofastq/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faToFastq && make) -cp bin/faToFastq "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToFastq" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faToFastq && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faToFastq "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faToFastq" diff --git a/recipes/ucsc-fatofastq/include.patch b/recipes/ucsc-fatofastq/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatofastq/include.patch +++ b/recipes/ucsc-fatofastq/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatofastq/meta.yaml b/recipes/ucsc-fatofastq/meta.yaml index 31b3b7709b9d3..e2ecba2ff9675 100644 --- a/recipes/ucsc-fatofastq/meta.yaml +++ b/recipes/ucsc-fatofastq/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatofastq" %} {% set program = "faToFastq" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert fa to fastq format, just faking quality values." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fatotab/build.sh b/recipes/ucsc-fatotab/build.sh index 6bdeebad8ed7b..1939aa14b9372 100644 --- a/recipes/ucsc-fatotab/build.sh +++ b/recipes/ucsc-fatotab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faToTab && make) -cp bin/faToTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faToTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faToTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faToTab" diff --git a/recipes/ucsc-fatotab/include.patch b/recipes/ucsc-fatotab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatotab/include.patch +++ b/recipes/ucsc-fatotab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatotab/meta.yaml b/recipes/ucsc-fatotab/meta.yaml index a5106bdd93cd2..c7901931785a1 100644 --- a/recipes/ucsc-fatotab/meta.yaml +++ b/recipes/ucsc-fatotab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatotab" %} {% set program = "faToTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert fa file to tab separated file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fatotwobit/build.sh b/recipes/ucsc-fatotwobit/build.sh index cd1c569ec1e88..73a564f9b469b 100644 --- a/recipes/ucsc-fatotwobit/build.sh +++ b/recipes/ucsc-fatotwobit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faToTwoBit && make) -cp bin/faToTwoBit "$PREFIX/bin" -chmod +x "$PREFIX/bin/faToTwoBit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faToTwoBit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faToTwoBit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faToTwoBit" diff --git a/recipes/ucsc-fatotwobit/include.patch b/recipes/ucsc-fatotwobit/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatotwobit/include.patch +++ b/recipes/ucsc-fatotwobit/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml index 4a21a851c4e54..0958911a7bf1d 100644 --- a/recipes/ucsc-fatotwobit/meta.yaml +++ b/recipes/ucsc-fatotwobit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatotwobit" %} {% set program = "faToTwoBit" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -12,46 +12,46 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" - - htmshell.patch build: - skip: True # [osx] - number: 2 - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage("ucsc-fatotwobit", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - - zlib >=1.3.1,<2.0a0 + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert DNA from fasta to 2bit format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-fatrans/build.sh b/recipes/ucsc-fatrans/build.sh index a781ab3d9c5fb..2e4768dfe353f 100644 --- a/recipes/ucsc-fatrans/build.sh +++ b/recipes/ucsc-fatrans/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/faTrans && make) -cp bin/faTrans "$PREFIX/bin" -chmod +x "$PREFIX/bin/faTrans" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/faTrans && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/faTrans "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/faTrans" diff --git a/recipes/ucsc-fatrans/include.patch b/recipes/ucsc-fatrans/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-fatrans/include.patch +++ b/recipes/ucsc-fatrans/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fatrans/meta.yaml b/recipes/ucsc-fatrans/meta.yaml index 39e117aec53d2..51811a6159fa7 100644 --- a/recipes/ucsc-fatrans/meta.yaml +++ b/recipes/ucsc-fatrans/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fatrans" %} {% set program = "faTrans" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Translate DNA .fa file to peptide" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-featurebits/build.sh b/recipes/ucsc-featurebits/build.sh index 0aab0a6b5bf92..917a51e28eb88 100644 --- a/recipes/ucsc-featurebits/build.sh +++ b/recipes/ucsc-featurebits/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/featureBits && make) -cp bin/featureBits "$PREFIX/bin" -chmod +x "$PREFIX/bin/featureBits" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/featureBits && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/featureBits "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/featureBits" diff --git a/recipes/ucsc-featurebits/include.patch b/recipes/ucsc-featurebits/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-featurebits/include.patch +++ b/recipes/ucsc-featurebits/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-featurebits/meta.yaml b/recipes/ucsc-featurebits/meta.yaml index 24e41aeb3841b..be467c8101577 100644 --- a/recipes/ucsc-featurebits/meta.yaml +++ b/recipes/ucsc-featurebits/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-featurebits" %} {% set program = "featureBits" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Correlate tables via bitmap projections. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-fetchchromsizes/build.sh b/recipes/ucsc-fetchchromsizes/build.sh index 60cb967c7e192..f37dd6327039f 100644 --- a/recipes/ucsc-fetchchromsizes/build.sh +++ b/recipes/ucsc-fetchchromsizes/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -mkdir -p $PREFIX/bin +set -xe -cp -f kent/src/utils/userApps/fetchChromSizes $PREFIX/bin -chmod 0755 $PREFIX/bin/fetchChromSizes +cp kent/src/utils/userApps/fetchChromSizes ${PREFIX}/bin +chmod 0755 ${PREFIX}/bin/fetchChromSizes diff --git a/recipes/ucsc-fetchchromsizes/include.patch b/recipes/ucsc-fetchchromsizes/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-fetchchromsizes/include.patch +++ b/recipes/ucsc-fetchchromsizes/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-fetchchromsizes/meta.yaml b/recipes/ucsc-fetchchromsizes/meta.yaml index e93d20580f61f..cfe061d194d38 100644 --- a/recipes/ucsc-fetchchromsizes/meta.yaml +++ b/recipes/ucsc-fetchchromsizes/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-fetchchromsizes" %} {% set program = "fetchChromSizes" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,26 +14,28 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-fetchchromsizes', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -42,7 +44,7 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: " used to fetch chrom.sizes information from UCSC for the given " @@ -50,5 +52,8 @@ used to fetch chrom.sizes information from UCSC for the given doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-findmotif/build.sh b/recipes/ucsc-findmotif/build.sh index c83f19994c25b..e0a729b566822 100644 --- a/recipes/ucsc-findmotif/build.sh +++ b/recipes/ucsc-findmotif/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/findMotif && make) -cp bin/findMotif "$PREFIX/bin" -chmod +x "$PREFIX/bin/findMotif" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/findMotif && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/findMotif "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/findMotif" diff --git a/recipes/ucsc-findmotif/include.patch b/recipes/ucsc-findmotif/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-findmotif/include.patch +++ b/recipes/ucsc-findmotif/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-findmotif/meta.yaml b/recipes/ucsc-findmotif/meta.yaml index 3ad718a71fc72..7a216c91b07df 100644 --- a/recipes/ucsc-findmotif/meta.yaml +++ b/recipes/ucsc-findmotif/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-findmotif" %} {% set program = "findMotif" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "find specified motif in sequence" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gaptolift/build.sh b/recipes/ucsc-gaptolift/build.sh index ed5e7af6dd119..3e35b9508f85a 100644 --- a/recipes/ucsc-gaptolift/build.sh +++ b/recipes/ucsc-gaptolift/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/gapToLift && make) -cp bin/gapToLift "$PREFIX/bin" -chmod +x "$PREFIX/bin/gapToLift" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gapToLift && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gapToLift "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gapToLift" diff --git a/recipes/ucsc-gaptolift/include.patch b/recipes/ucsc-gaptolift/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gaptolift/include.patch +++ b/recipes/ucsc-gaptolift/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gaptolift/meta.yaml b/recipes/ucsc-gaptolift/meta.yaml index b30683d4565e8..c507cae4e79c9 100644 --- a/recipes/ucsc-gaptolift/meta.yaml +++ b/recipes/ucsc-gaptolift/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gaptolift" %} {% set program = "gapToLift" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create lift file from gap table(s)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-genepredcheck/build.sh b/recipes/ucsc-genepredcheck/build.sh index b6524788d6ce9..2e78923fd14a7 100644 --- a/recipes/ucsc-genepredcheck/build.sh +++ b/recipes/ucsc-genepredcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/genePredCheck && make -j ${CPU_COUNT}) -cp bin/genePredCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredCheck" diff --git a/recipes/ucsc-genepredcheck/include.patch b/recipes/ucsc-genepredcheck/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredcheck/include.patch +++ b/recipes/ucsc-genepredcheck/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-genepredcheck/meta.yaml b/recipes/ucsc-genepredcheck/meta.yaml index 3431a4e7693ad..7cb175e5b7391 100644 --- a/recipes/ucsc-genepredcheck/meta.yaml +++ b/recipes/ucsc-genepredcheck/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-genepredcheck" %} {% set program = "genePredCheck" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: # just check for existence and exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Validate genePred files or tables" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "validate genePred files or tables" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-genepredfilter/build.sh b/recipes/ucsc-genepredfilter/build.sh index 740a38a92b847..43aedb3dafe58 100644 --- a/recipes/ucsc-genepredfilter/build.sh +++ b/recipes/ucsc-genepredfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/genePredFilter && make) -cp bin/genePredFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/genePredFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredFilter" diff --git a/recipes/ucsc-genepredfilter/include.patch b/recipes/ucsc-genepredfilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredfilter/include.patch +++ b/recipes/ucsc-genepredfilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredfilter/meta.yaml b/recipes/ucsc-genepredfilter/meta.yaml index bbdbe7224a9b2..856ecec5c55d7 100644 --- a/recipes/ucsc-genepredfilter/meta.yaml +++ b/recipes/ucsc-genepredfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredfilter" %} {% set program = "genePredFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "filter a genePred file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-genepredhisto/build.sh b/recipes/ucsc-genepredhisto/build.sh index eae0a8415e1ce..7cbdc5550a941 100644 --- a/recipes/ucsc-genepredhisto/build.sh +++ b/recipes/ucsc-genepredhisto/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredHisto && make) -cp bin/genePredHisto "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredHisto" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredHisto && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredHisto "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredHisto" diff --git a/recipes/ucsc-genepredhisto/include.patch b/recipes/ucsc-genepredhisto/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredhisto/include.patch +++ b/recipes/ucsc-genepredhisto/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredhisto/meta.yaml b/recipes/ucsc-genepredhisto/meta.yaml index 2c5afb13865f9..da938e08e703b 100644 --- a/recipes/ucsc-genepredhisto/meta.yaml +++ b/recipes/ucsc-genepredhisto/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredhisto" %} {% set program = "genePredHisto" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get data for generating histograms from a genePred file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-genepredsinglecover/build.sh b/recipes/ucsc-genepredsinglecover/build.sh index cc6aa8cdea7b8..69a1610ac29a2 100644 --- a/recipes/ucsc-genepredsinglecover/build.sh +++ b/recipes/ucsc-genepredsinglecover/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredSingleCover && make) -cp bin/genePredSingleCover "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredSingleCover" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredSingleCover && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredSingleCover "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredSingleCover" diff --git a/recipes/ucsc-genepredsinglecover/include.patch b/recipes/ucsc-genepredsinglecover/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredsinglecover/include.patch +++ b/recipes/ucsc-genepredsinglecover/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredsinglecover/meta.yaml b/recipes/ucsc-genepredsinglecover/meta.yaml index c5feab4138c2a..b25766645d545 100644 --- a/recipes/ucsc-genepredsinglecover/meta.yaml +++ b/recipes/ucsc-genepredsinglecover/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredsinglecover" %} {% set program = "genePredSingleCover" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create single-coverage genePred files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-genepredtobed/build.sh b/recipes/ucsc-genepredtobed/build.sh index 73f68a12d7a6a..c2d189f5935c0 100644 --- a/recipes/ucsc-genepredtobed/build.sh +++ b/recipes/ucsc-genepredtobed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredToBed && make) -cp bin/genePredToBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToBed" diff --git a/recipes/ucsc-genepredtobed/include.patch b/recipes/ucsc-genepredtobed/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtobed/include.patch +++ b/recipes/ucsc-genepredtobed/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-genepredtobed/meta.yaml b/recipes/ucsc-genepredtobed/meta.yaml index ce54339cf9111..c444a3219e8cc 100644 --- a/recipes/ucsc-genepredtobed/meta.yaml +++ b/recipes/ucsc-genepredtobed/meta.yaml @@ -1,25 +1,21 @@ {% set package = "ucsc-genepredtobed" %} {% set program = "genePredToBed" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from genePred to bed format. Does not yet handle genePredExt" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-genepredtobiggenepred/build.sh b/recipes/ucsc-genepredtobiggenepred/build.sh index baf17c6b537f2..22cb9a1a3f13f 100644 --- a/recipes/ucsc-genepredtobiggenepred/build.sh +++ b/recipes/ucsc-genepredtobiggenepred/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/genePredToBigGenePred && make -j ${CPU_COUNT}) -cp bin/genePredToBigGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToBigGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/genePredToBigGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToBigGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToBigGenePred" diff --git a/recipes/ucsc-genepredtobiggenepred/include.patch b/recipes/ucsc-genepredtobiggenepred/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtobiggenepred/include.patch +++ b/recipes/ucsc-genepredtobiggenepred/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-genepredtobiggenepred/meta.yaml b/recipes/ucsc-genepredtobiggenepred/meta.yaml index 7c13583979a71..29be5b867754b 100644 --- a/recipes/ucsc-genepredtobiggenepred/meta.yaml +++ b/recipes/ucsc-genepredtobiggenepred/meta.yaml @@ -1,46 +1,41 @@ {% set package = "ucsc-genepredtobiggenepred" %} {% set program = "genePredToBigGenePred" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: @@ -48,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Converts genePred or genePredExt to bigGenePred input (bed format with extra fields)" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "converts genePred or genePredExt to bigGenePred input (bed format with extra fields)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-genepredtofakepsl/build.sh b/recipes/ucsc-genepredtofakepsl/build.sh index 03cf481ed9fae..0cbaf2644b10f 100644 --- a/recipes/ucsc-genepredtofakepsl/build.sh +++ b/recipes/ucsc-genepredtofakepsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredToFakePsl && make) -cp bin/genePredToFakePsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToFakePsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToFakePsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToFakePsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToFakePsl" diff --git a/recipes/ucsc-genepredtofakepsl/include.patch b/recipes/ucsc-genepredtofakepsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtofakepsl/include.patch +++ b/recipes/ucsc-genepredtofakepsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredtofakepsl/meta.yaml b/recipes/ucsc-genepredtofakepsl/meta.yaml index 6dd0dbfb20747..96c1f50452bcb 100644 --- a/recipes/ucsc-genepredtofakepsl/meta.yaml +++ b/recipes/ucsc-genepredtofakepsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtofakepsl" %} {% set program = "genePredToFakePsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create a psl of fake-mRNA aligned to gene-preds from a file or table." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-genepredtogtf/build.sh b/recipes/ucsc-genepredtogtf/build.sh index 626b3eed43b01..2eacfa5aca0fe 100644 --- a/recipes/ucsc-genepredtogtf/build.sh +++ b/recipes/ucsc-genepredtogtf/build.sh @@ -2,15 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && USE_HIC=0 make -j ${CPU_COUNT}) -(cd kent/src/hg/genePredToGtf && make -j ${CPU_COUNT}) -cp bin/genePredToGtf "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToGtf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToGtf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToGtf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToGtf" diff --git a/recipes/ucsc-genepredtogtf/include.patch b/recipes/ucsc-genepredtogtf/include.patch index e2c7f6e6cb70a..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtogtf/include.patch +++ b/recipes/ucsc-genepredtogtf/include.patch @@ -5,7 +5,7 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) diff --git a/recipes/ucsc-genepredtogtf/meta.yaml b/recipes/ucsc-genepredtogtf/meta.yaml index 4283d807812f0..b305f23ca4929 100644 --- a/recipes/ucsc-genepredtogtf/meta.yaml +++ b/recipes/ucsc-genepredtogtf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtogtf" %} {% set program = "genePredToGtf" %} -{% set version = "465" %} -{% set sha256 = "eef17b1f3182d1d9dc99b5c73a6b0468d5d3bd80470f25d3f7706cc1372e04b0" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,10 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert genePred table or file to gtf." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-genepredtomafframes/build.sh b/recipes/ucsc-genepredtomafframes/build.sh index 3c6c10a9fad99..d0914e9e23d2e 100644 --- a/recipes/ucsc-genepredtomafframes/build.sh +++ b/recipes/ucsc-genepredtomafframes/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/genePredToMafFrames && make) -cp bin/genePredToMafFrames "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToMafFrames" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/genePredToMafFrames && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToMafFrames "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToMafFrames" diff --git a/recipes/ucsc-genepredtomafframes/include.patch b/recipes/ucsc-genepredtomafframes/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtomafframes/include.patch +++ b/recipes/ucsc-genepredtomafframes/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredtomafframes/meta.yaml b/recipes/ucsc-genepredtomafframes/meta.yaml index de319b6994200..56bc3ddd8238d 100644 --- a/recipes/ucsc-genepredtomafframes/meta.yaml +++ b/recipes/ucsc-genepredtomafframes/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtomafframes" %} {% set program = "genePredToMafFrames" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create mafFrames tables from a genePreds" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-genepredtoprot/build.sh b/recipes/ucsc-genepredtoprot/build.sh index 45cad43fa314d..0e997669e739d 100644 --- a/recipes/ucsc-genepredtoprot/build.sh +++ b/recipes/ucsc-genepredtoprot/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/genePredToProt && make) -cp bin/genePredToProt "$PREFIX/bin" -chmod +x "$PREFIX/bin/genePredToProt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/genePredToProt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/genePredToProt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/genePredToProt" diff --git a/recipes/ucsc-genepredtoprot/include.patch b/recipes/ucsc-genepredtoprot/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-genepredtoprot/include.patch +++ b/recipes/ucsc-genepredtoprot/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-genepredtoprot/meta.yaml b/recipes/ucsc-genepredtoprot/meta.yaml index b04d00344ff6f..8f0816e7c00dd 100644 --- a/recipes/ucsc-genepredtoprot/meta.yaml +++ b/recipes/ucsc-genepredtoprot/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-genepredtoprot" %} {% set program = "genePredToProt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create protein sequences by translating gene annotations" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gensub2/build.sh b/recipes/ucsc-gensub2/build.sh index c2fb30cfe1ea8..7eea99522dd3e 100644 --- a/recipes/ucsc-gensub2/build.sh +++ b/recipes/ucsc-gensub2/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/gensub2 "$PREFIX/bin" -chmod +x "$PREFIX/bin/gensub2" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/gensub2 "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gensub2" diff --git a/recipes/ucsc-gensub2/include.patch b/recipes/ucsc-gensub2/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gensub2/include.patch +++ b/recipes/ucsc-gensub2/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gensub2/meta.yaml b/recipes/ucsc-gensub2/meta.yaml index 9dbd6efb84cd5..5b1d1ebc67a8d 100644 --- a/recipes/ucsc-gensub2/meta.yaml +++ b/recipes/ucsc-gensub2/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gensub2" %} {% set program = "gensub2" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-getrna/build.sh b/recipes/ucsc-getrna/build.sh index a143abd3f5d49..68c77a40cd7d3 100644 --- a/recipes/ucsc-getrna/build.sh +++ b/recipes/ucsc-getrna/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/getRna && make) -cp bin/getRna "$PREFIX/bin" -chmod +x "$PREFIX/bin/getRna" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/getRna && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/getRna "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/getRna" diff --git a/recipes/ucsc-getrna/include.patch b/recipes/ucsc-getrna/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-getrna/include.patch +++ b/recipes/ucsc-getrna/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-getrna/meta.yaml b/recipes/ucsc-getrna/meta.yaml index 2762bd242def6..37dda84b17d32 100644 --- a/recipes/ucsc-getrna/meta.yaml +++ b/recipes/ucsc-getrna/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-getrna" %} {% set program = "getRna" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get mrna for GenBank or RefSeq sequences found in a database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-getrnapred/build.sh b/recipes/ucsc-getrnapred/build.sh index 8fc3876e2eba3..1285faed92b52 100644 --- a/recipes/ucsc-getrnapred/build.sh +++ b/recipes/ucsc-getrnapred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/getRnaPred && make) -cp bin/getRnaPred "$PREFIX/bin" -chmod +x "$PREFIX/bin/getRnaPred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/getRnaPred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/getRnaPred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/getRnaPred" diff --git a/recipes/ucsc-getrnapred/include.patch b/recipes/ucsc-getrnapred/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-getrnapred/include.patch +++ b/recipes/ucsc-getrnapred/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-getrnapred/meta.yaml b/recipes/ucsc-getrnapred/meta.yaml index 456e7a2e36ce1..fa521485d5276 100644 --- a/recipes/ucsc-getrnapred/meta.yaml +++ b/recipes/ucsc-getrnapred/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-getrnapred" %} {% set program = "getRnaPred" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Get virtual RNA for gene predictions" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gff3togenepred/build.sh b/recipes/ucsc-gff3togenepred/build.sh index 6ffa740fe32c1..98a30d0537b93 100644 --- a/recipes/ucsc-gff3togenepred/build.sh +++ b/recipes/ucsc-gff3togenepred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/utils/gff3ToGenePred && make -j ${CPU_COUNT}) -cp bin/gff3ToGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/gff3ToGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gff3ToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gff3ToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gff3ToGenePred" diff --git a/recipes/ucsc-gff3togenepred/include.patch b/recipes/ucsc-gff3togenepred/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-gff3togenepred/include.patch +++ b/recipes/ucsc-gff3togenepred/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-gff3togenepred/meta.yaml b/recipes/ucsc-gff3togenepred/meta.yaml index 184186af9a4d2..e47309c9e4364 100644 --- a/recipes/ucsc-gff3togenepred/meta.yaml +++ b/recipes/ucsc-gff3togenepred/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-gff3togenepred" %} {% set program = "gff3ToGenePred" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: # just check for existence and exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert a GFF3 file to a genePred file" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "convert a GFF3 file to a genePred file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-gff3topsl/build.sh b/recipes/ucsc-gff3topsl/build.sh index 0af0b67a67fa0..1480a1a5c4c6c 100644 --- a/recipes/ucsc-gff3topsl/build.sh +++ b/recipes/ucsc-gff3topsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/gff3ToPsl && make) -cp bin/gff3ToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/gff3ToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gff3ToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gff3ToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gff3ToPsl" diff --git a/recipes/ucsc-gff3topsl/include.patch b/recipes/ucsc-gff3topsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gff3topsl/include.patch +++ b/recipes/ucsc-gff3topsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gff3topsl/meta.yaml b/recipes/ucsc-gff3topsl/meta.yaml index 4a1ea66855d54..6b6d7a265cea8 100644 --- a/recipes/ucsc-gff3topsl/meta.yaml +++ b/recipes/ucsc-gff3topsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gff3topsl" %} {% set program = "gff3ToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert a GFF3 CIGAR file to a PSL file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gmtime/build.sh b/recipes/ucsc-gmtime/build.sh index df84f2bc8be6f..f9fdd83658185 100644 --- a/recipes/ucsc-gmtime/build.sh +++ b/recipes/ucsc-gmtime/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/timing/gmtime && make) -cp bin/gmtime "$PREFIX/bin" -chmod +x "$PREFIX/bin/gmtime" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/timing/gmtime && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gmtime "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gmtime" diff --git a/recipes/ucsc-gmtime/include.patch b/recipes/ucsc-gmtime/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-gmtime/include.patch +++ b/recipes/ucsc-gmtime/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-gmtime/meta.yaml b/recipes/ucsc-gmtime/meta.yaml index 3a363611db7b8..be7f2efb84739 100644 --- a/recipes/ucsc-gmtime/meta.yaml +++ b/recipes/ucsc-gmtime/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-gmtime" %} {% set program = "gmtime" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert unix timestamp to date string" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-gtftogenepred/build.sh b/recipes/ucsc-gtftogenepred/build.sh index 49f68076bbb2e..80a3ce55a4aa6 100644 --- a/recipes/ucsc-gtftogenepred/build.sh +++ b/recipes/ucsc-gtftogenepred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/gtfToGenePred && make) -cp bin/gtfToGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/gtfToGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/gtfToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/gtfToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/gtfToGenePred" diff --git a/recipes/ucsc-gtftogenepred/include.patch b/recipes/ucsc-gtftogenepred/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-gtftogenepred/include.patch +++ b/recipes/ucsc-gtftogenepred/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-gtftogenepred/meta.yaml b/recipes/ucsc-gtftogenepred/meta.yaml index 87ed2f492e9cb..b62f391a82aa4 100644 --- a/recipes/ucsc-gtftogenepred/meta.yaml +++ b/recipes/ucsc-gtftogenepred/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-gtftogenepred" %} {% set program = "gtfToGenePred" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage(package|lower, max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert a GTF file to a genePred" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "convert a GTF file to a genePred" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-headrest/build.sh b/recipes/ucsc-headrest/build.sh index e663809978aba..42931e2fdcda4 100644 --- a/recipes/ucsc-headrest/build.sh +++ b/recipes/ucsc-headrest/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/headRest && make) -cp bin/headRest "$PREFIX/bin" -chmod +x "$PREFIX/bin/headRest" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/headRest && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/headRest "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/headRest" diff --git a/recipes/ucsc-headrest/include.patch b/recipes/ucsc-headrest/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-headrest/include.patch +++ b/recipes/ucsc-headrest/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-headrest/meta.yaml b/recipes/ucsc-headrest/meta.yaml index ca8f56ff645ef..5544ab7e8edc7 100644 --- a/recipes/ucsc-headrest/meta.yaml +++ b/recipes/ucsc-headrest/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-headrest" %} {% set program = "headRest" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Return all *but* the first N lines of a file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgbbidblink/build.sh b/recipes/ucsc-hgbbidblink/build.sh index 6da58add15c6a..bd30d4f90abf3 100644 --- a/recipes/ucsc-hgbbidblink/build.sh +++ b/recipes/ucsc-hgbbidblink/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgBbiDbLink && make) -cp bin/hgBbiDbLink "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgBbiDbLink" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgBbiDbLink && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgBbiDbLink "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgBbiDbLink" diff --git a/recipes/ucsc-hgbbidblink/include.patch b/recipes/ucsc-hgbbidblink/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgbbidblink/include.patch +++ b/recipes/ucsc-hgbbidblink/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgbbidblink/meta.yaml b/recipes/ucsc-hgbbidblink/meta.yaml index b1ad270d2c719..45c299a6c87ee 100644 --- a/recipes/ucsc-hgbbidblink/meta.yaml +++ b/recipes/ucsc-hgbbidblink/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgbbidblink" %} {% set program = "hgBbiDbLink" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add table that just contains a pointer to a bbiFile to database. This program " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgfakeagp/build.sh b/recipes/ucsc-hgfakeagp/build.sh index da41fc2e586e1..03d106363c3f0 100644 --- a/recipes/ucsc-hgfakeagp/build.sh +++ b/recipes/ucsc-hgfakeagp/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgFakeAgp && make) -cp bin/hgFakeAgp "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgFakeAgp" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgFakeAgp && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgFakeAgp "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgFakeAgp" diff --git a/recipes/ucsc-hgfakeagp/include.patch b/recipes/ucsc-hgfakeagp/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgfakeagp/include.patch +++ b/recipes/ucsc-hgfakeagp/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgfakeagp/meta.yaml b/recipes/ucsc-hgfakeagp/meta.yaml index a8f5f3d17ac1e..457365f7fa59a 100644 --- a/recipes/ucsc-hgfakeagp/meta.yaml +++ b/recipes/ucsc-hgfakeagp/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgfakeagp" %} {% set program = "hgFakeAgp" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create fake AGP file by looking at N's" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgfindspec/build.sh b/recipes/ucsc-hgfindspec/build.sh index 86c10fc48027c..f02b401cba046 100644 --- a/recipes/ucsc-hgfindspec/build.sh +++ b/recipes/ucsc-hgfindspec/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgFindSpec && make) -cp bin/hgFindSpec "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgFindSpec" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgFindSpec && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgFindSpec "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgFindSpec" diff --git a/recipes/ucsc-hgfindspec/include.patch b/recipes/ucsc-hgfindspec/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgfindspec/include.patch +++ b/recipes/ucsc-hgfindspec/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgfindspec/meta.yaml b/recipes/ucsc-hgfindspec/meta.yaml index fa2b4eca2f34b..5d58a135b1576 100644 --- a/recipes/ucsc-hgfindspec/meta.yaml +++ b/recipes/ucsc-hgfindspec/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgfindspec" %} {% set program = "hgFindSpec" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create hgFindSpec table from trackDb.ra files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hggcpercent/build.sh b/recipes/ucsc-hggcpercent/build.sh index 769b86221d65f..0f13041348d4e 100644 --- a/recipes/ucsc-hggcpercent/build.sh +++ b/recipes/ucsc-hggcpercent/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/hg/makeDb/hgGcPercent && make -j ${CPU_COUNT}) -cp bin/hgGcPercent "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgGcPercent" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgGcPercent && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgGcPercent "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgGcPercent" diff --git a/recipes/ucsc-hggcpercent/include.patch b/recipes/ucsc-hggcpercent/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-hggcpercent/include.patch +++ b/recipes/ucsc-hggcpercent/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-hggcpercent/meta.yaml b/recipes/ucsc-hggcpercent/meta.yaml index 9317978520057..c2fc70c43fa1f 100644 --- a/recipes/ucsc-hggcpercent/meta.yaml +++ b/recipes/ucsc-hggcpercent/meta.yaml @@ -1,22 +1,21 @@ {% set package = "ucsc-hggcpercent" %} {% set program = "hgGcPercent" %} -{% set version = "448" %} -{% set sha256 = "90c28f06f3f5b6d79ff141cbf745e6a0c1b289a2ce640bbd1b0a14c826f08a85" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: - url: http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz - sha256: {{ sha256 }} + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -24,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: # just check for existence and exec bit, because the individual packages have no unified behavior - - test -x $PREFIX/bin/{{ program }} + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Calculate GC Percentage in 20kb windows" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-hgloadbed/build.sh b/recipes/ucsc-hgloadbed/build.sh index 6c0b79016fe23..62d56d66a98c7 100644 --- a/recipes/ucsc-hgloadbed/build.sh +++ b/recipes/ucsc-hgloadbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadBed && make) -cp bin/hgLoadBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadBed" diff --git a/recipes/ucsc-hgloadbed/include.patch b/recipes/ucsc-hgloadbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadbed/include.patch +++ b/recipes/ucsc-hgloadbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadbed/meta.yaml b/recipes/ucsc-hgloadbed/meta.yaml index c14a6b24bfc5f..f28a37518d1b7 100644 --- a/recipes/ucsc-hgloadbed/meta.yaml +++ b/recipes/ucsc-hgloadbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadbed" %} {% set program = "hgLoadBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a generic bed file into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadchain/build.sh b/recipes/ucsc-hgloadchain/build.sh index 7733176a98e61..0836ef0a2b3a4 100644 --- a/recipes/ucsc-hgloadchain/build.sh +++ b/recipes/ucsc-hgloadchain/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadChain && make) -cp bin/hgLoadChain "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadChain" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadChain" diff --git a/recipes/ucsc-hgloadchain/include.patch b/recipes/ucsc-hgloadchain/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadchain/include.patch +++ b/recipes/ucsc-hgloadchain/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadchain/meta.yaml b/recipes/ucsc-hgloadchain/meta.yaml index a37db8bb33d55..6dc6fcd9cd48e 100644 --- a/recipes/ucsc-hgloadchain/meta.yaml +++ b/recipes/ucsc-hgloadchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadchain" %} {% set program = "hgLoadChain" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a generic Chain file into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadmaf/build.sh b/recipes/ucsc-hgloadmaf/build.sh index 2ae0cbe492abd..6e858c951b003 100644 --- a/recipes/ucsc-hgloadmaf/build.sh +++ b/recipes/ucsc-hgloadmaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadMaf && make) -cp bin/hgLoadMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadMaf" diff --git a/recipes/ucsc-hgloadmaf/include.patch b/recipes/ucsc-hgloadmaf/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadmaf/include.patch +++ b/recipes/ucsc-hgloadmaf/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadmaf/meta.yaml b/recipes/ucsc-hgloadmaf/meta.yaml index 19b53f7e81296..5d02740d43f93 100644 --- a/recipes/ucsc-hgloadmaf/meta.yaml +++ b/recipes/ucsc-hgloadmaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadmaf" %} {% set program = "hgLoadMaf" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a maf file index into the database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadnet/build.sh b/recipes/ucsc-hgloadnet/build.sh index afd005fbf3b31..44361aee149dc 100644 --- a/recipes/ucsc-hgloadnet/build.sh +++ b/recipes/ucsc-hgloadnet/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadNet && make) -cp bin/hgLoadNet "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadNet" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadNet && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadNet "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadNet" diff --git a/recipes/ucsc-hgloadnet/include.patch b/recipes/ucsc-hgloadnet/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadnet/include.patch +++ b/recipes/ucsc-hgloadnet/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadnet/meta.yaml b/recipes/ucsc-hgloadnet/meta.yaml index 29d2d37aa891a..13e998111031a 100644 --- a/recipes/ucsc-hgloadnet/meta.yaml +++ b/recipes/ucsc-hgloadnet/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadnet" %} {% set program = "hgLoadNet" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a generic net file into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadout/build.sh b/recipes/ucsc-hgloadout/build.sh index bcbdfa0686952..19021359dacaf 100644 --- a/recipes/ucsc-hgloadout/build.sh +++ b/recipes/ucsc-hgloadout/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadOut && make) -cp bin/hgLoadOut "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadOut" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadOut && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadOut "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadOut" diff --git a/recipes/ucsc-hgloadout/include.patch b/recipes/ucsc-hgloadout/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadout/include.patch +++ b/recipes/ucsc-hgloadout/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadout/meta.yaml b/recipes/ucsc-hgloadout/meta.yaml index 589de17eb66f8..b85a76f593a43 100644 --- a/recipes/ucsc-hgloadout/meta.yaml +++ b/recipes/ucsc-hgloadout/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadout" %} {% set program = "hgLoadOut" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "load RepeatMasker .out files into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadoutjoined/build.sh b/recipes/ucsc-hgloadoutjoined/build.sh index 52f973bd6094f..1dd85c8321304 100644 --- a/recipes/ucsc-hgloadoutjoined/build.sh +++ b/recipes/ucsc-hgloadoutjoined/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadOutJoined && make) -cp bin/hgLoadOutJoined "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadOutJoined" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadOutJoined && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadOutJoined "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadOutJoined" diff --git a/recipes/ucsc-hgloadoutjoined/include.patch b/recipes/ucsc-hgloadoutjoined/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadoutjoined/include.patch +++ b/recipes/ucsc-hgloadoutjoined/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadoutjoined/meta.yaml b/recipes/ucsc-hgloadoutjoined/meta.yaml index 7a8f58d48adf8..9e269f7ccfc88 100644 --- a/recipes/ucsc-hgloadoutjoined/meta.yaml +++ b/recipes/ucsc-hgloadoutjoined/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadoutjoined" %} {% set program = "hgLoadOutJoined" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "load new style (2014) RepeatMasker .out files into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadsqltab/build.sh b/recipes/ucsc-hgloadsqltab/build.sh index 6b583d73e1561..943bf9b400cec 100644 --- a/recipes/ucsc-hgloadsqltab/build.sh +++ b/recipes/ucsc-hgloadsqltab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadSqlTab && make) -cp bin/hgLoadSqlTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadSqlTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadSqlTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadSqlTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadSqlTab" diff --git a/recipes/ucsc-hgloadsqltab/include.patch b/recipes/ucsc-hgloadsqltab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadsqltab/include.patch +++ b/recipes/ucsc-hgloadsqltab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadsqltab/meta.yaml b/recipes/ucsc-hgloadsqltab/meta.yaml index a66bbbbb50a27..1ae390c3c6a3f 100644 --- a/recipes/ucsc-hgloadsqltab/meta.yaml +++ b/recipes/ucsc-hgloadsqltab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadsqltab" %} {% set program = "hgLoadSqlTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load table into database from SQL and text files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgloadwiggle/build.sh b/recipes/ucsc-hgloadwiggle/build.sh index 8530d3cc9a930..5a8736a672f80 100644 --- a/recipes/ucsc-hgloadwiggle/build.sh +++ b/recipes/ucsc-hgloadwiggle/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgLoadWiggle && make) -cp bin/hgLoadWiggle "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgLoadWiggle" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgLoadWiggle && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgLoadWiggle "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgLoadWiggle" diff --git a/recipes/ucsc-hgloadwiggle/include.patch b/recipes/ucsc-hgloadwiggle/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgloadwiggle/include.patch +++ b/recipes/ucsc-hgloadwiggle/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgloadwiggle/meta.yaml b/recipes/ucsc-hgloadwiggle/meta.yaml index 6859a90c405b5..2f1914ae2a533 100644 --- a/recipes/ucsc-hgloadwiggle/meta.yaml +++ b/recipes/ucsc-hgloadwiggle/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgloadwiggle" %} {% set program = "hgLoadWiggle" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Load a wiggle track definition into database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgspeciesrna/build.sh b/recipes/ucsc-hgspeciesrna/build.sh index b6858f027c0a5..1af260d069942 100644 --- a/recipes/ucsc-hgspeciesrna/build.sh +++ b/recipes/ucsc-hgspeciesrna/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/hgSpeciesRna && make) -cp bin/hgSpeciesRna "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgSpeciesRna" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/hgSpeciesRna && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgSpeciesRna "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgSpeciesRna" diff --git a/recipes/ucsc-hgspeciesrna/include.patch b/recipes/ucsc-hgspeciesrna/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgspeciesrna/include.patch +++ b/recipes/ucsc-hgspeciesrna/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgspeciesrna/meta.yaml b/recipes/ucsc-hgspeciesrna/meta.yaml index 5970a38722898..68f1e4bce6249 100644 --- a/recipes/ucsc-hgspeciesrna/meta.yaml +++ b/recipes/ucsc-hgspeciesrna/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgspeciesrna" %} {% set program = "hgSpeciesRna" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create fasta file with RNA from one species" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgsqldump/build.sh b/recipes/ucsc-hgsqldump/build.sh index 80671787650fb..dbee464b271c9 100644 --- a/recipes/ucsc-hgsqldump/build.sh +++ b/recipes/ucsc-hgsqldump/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/hgsqldump && make) -cp bin/hgsqldump "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgsqldump" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/hgsqldump && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgsqldump "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgsqldump" diff --git a/recipes/ucsc-hgsqldump/include.patch b/recipes/ucsc-hgsqldump/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgsqldump/include.patch +++ b/recipes/ucsc-hgsqldump/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgsqldump/meta.yaml b/recipes/ucsc-hgsqldump/meta.yaml index 9b1ffe0672543..cf837117dbedc 100644 --- a/recipes/ucsc-hgsqldump/meta.yaml +++ b/recipes/ucsc-hgsqldump/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgsqldump" %} {% set program = "hgsqldump" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Execute mysqldump using passwords from .hg.conf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hgtrackdb/build.sh b/recipes/ucsc-hgtrackdb/build.sh index e1b8ac6e65c4f..106bc9b2835e1 100644 --- a/recipes/ucsc-hgtrackdb/build.sh +++ b/recipes/ucsc-hgtrackdb/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/hgTrackDb && make) -cp bin/hgTrackDb "$PREFIX/bin" -chmod +x "$PREFIX/bin/hgTrackDb" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/hgTrackDb && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hgTrackDb "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hgTrackDb" diff --git a/recipes/ucsc-hgtrackdb/include.patch b/recipes/ucsc-hgtrackdb/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hgtrackdb/include.patch +++ b/recipes/ucsc-hgtrackdb/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hgtrackdb/meta.yaml b/recipes/ucsc-hgtrackdb/meta.yaml index dc17c36ddfcd2..3c71224c9c067 100644 --- a/recipes/ucsc-hgtrackdb/meta.yaml +++ b/recipes/ucsc-hgtrackdb/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hgtrackdb" %} {% set program = "hgTrackDb" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create trackDb table from text files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-htmlcheck/build.sh b/recipes/ucsc-htmlcheck/build.sh index b99b826297c80..10020a3222df5 100644 --- a/recipes/ucsc-htmlcheck/build.sh +++ b/recipes/ucsc-htmlcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/htmlCheck && make) -cp bin/htmlCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/htmlCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/htmlCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/htmlCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/htmlCheck" diff --git a/recipes/ucsc-htmlcheck/include.patch b/recipes/ucsc-htmlcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-htmlcheck/include.patch +++ b/recipes/ucsc-htmlcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-htmlcheck/meta.yaml b/recipes/ucsc-htmlcheck/meta.yaml index 2fb806db88e37..edc5c0b821f24 100644 --- a/recipes/ucsc-htmlcheck/meta.yaml +++ b/recipes/ucsc-htmlcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-htmlcheck" %} {% set program = "htmlCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Do a little reading and verification of html file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hubcheck/build.sh b/recipes/ucsc-hubcheck/build.sh index f680c4c42c14b..42f264921d821 100644 --- a/recipes/ucsc-hubcheck/build.sh +++ b/recipes/ucsc-hubcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/hubCheck && make) -cp bin/hubCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/hubCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/hubCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hubCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hubCheck" diff --git a/recipes/ucsc-hubcheck/include.patch b/recipes/ucsc-hubcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hubcheck/include.patch +++ b/recipes/ucsc-hubcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hubcheck/meta.yaml b/recipes/ucsc-hubcheck/meta.yaml index a7bbbafd799af..2375f5b24f2b6 100644 --- a/recipes/ucsc-hubcheck/meta.yaml +++ b/recipes/ucsc-hubcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hubcheck" %} {% set program = "hubCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Check a track data hub for integrity." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-hubpubliccheck/build.sh b/recipes/ucsc-hubpubliccheck/build.sh index e44de2a3b03aa..9e62440c60826 100644 --- a/recipes/ucsc-hubpubliccheck/build.sh +++ b/recipes/ucsc-hubpubliccheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/hubPublicCheck && make) -cp bin/hubPublicCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/hubPublicCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/hubPublicCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/hubPublicCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/hubPublicCheck" diff --git a/recipes/ucsc-hubpubliccheck/include.patch b/recipes/ucsc-hubpubliccheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-hubpubliccheck/include.patch +++ b/recipes/ucsc-hubpubliccheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-hubpubliccheck/meta.yaml b/recipes/ucsc-hubpubliccheck/meta.yaml index cca7bfbd24adb..c16300f30249c 100644 --- a/recipes/ucsc-hubpubliccheck/meta.yaml +++ b/recipes/ucsc-hubpubliccheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-hubpubliccheck" %} {% set program = "hubPublicCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "checks that the labels in hubPublic match what is in the hub labels" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ixixx/build.sh b/recipes/ucsc-ixixx/build.sh index e4ce4fe68f1ae..961320e7fd96d 100644 --- a/recipes/ucsc-ixixx/build.sh +++ b/recipes/ucsc-ixixx/build.sh @@ -1,5 +1,8 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" @@ -8,11 +11,11 @@ export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/index/ixIxx && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/ixIxx "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/ixIxx" +cp bin/ixIxx "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/ixIxx" diff --git a/recipes/ucsc-ixixx/include.patch b/recipes/ucsc-ixixx/include.patch index 1646de15a38f7..edc04d0dc2f64 100644 --- a/recipes/ucsc-ixixx/include.patch +++ b/recipes/ucsc-ixixx/include.patch @@ -1,5 +1,5 @@ ---- a/kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ b/kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 +--- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif @@ -9,16 +9,16 @@ # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- a/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python import logging, sys, optparse, string from collections import defaultdict ---- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 -+++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ixixx/meta.yaml b/recipes/ucsc-ixixx/meta.yaml index 67d8022a455c2..12e29c5de07c1 100644 --- a/recipes/ucsc-ixixx/meta.yaml +++ b/recipes/ucsc-ixixx/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ixixx" %} {% set program = "ixIxx" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,26 +14,28 @@ source: - "include.patch" build: + skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage('ucsc-ixixx', max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} host: - libpng - libuuid - mysql-connector-c - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - libopenssl-static + - zlib test: commands: @@ -42,11 +44,14 @@ test: about: home: "https://hgdownload.cse.ucsc.edu/admin/exe/" - license: "Varies; see https://genome.ucsc.edu/license" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create indices for simple line-oriented file of format " dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - linux-aarch64 diff --git a/recipes/ucsc-lavtoaxt/build.sh b/recipes/ucsc-lavtoaxt/build.sh index 053f95a6d6f0c..28b7382f0f659 100644 --- a/recipes/ucsc-lavtoaxt/build.sh +++ b/recipes/ucsc-lavtoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/lavToAxt && make) -cp bin/lavToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/lavToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/lavToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/lavToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/lavToAxt" diff --git a/recipes/ucsc-lavtoaxt/include.patch b/recipes/ucsc-lavtoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-lavtoaxt/include.patch +++ b/recipes/ucsc-lavtoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-lavtoaxt/meta.yaml b/recipes/ucsc-lavtoaxt/meta.yaml index e1c9793a5521a..06c0cafe88b92 100644 --- a/recipes/ucsc-lavtoaxt/meta.yaml +++ b/recipes/ucsc-lavtoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-lavtoaxt" %} {% set program = "lavToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert blastz lav file to an axt file (which includes sequence)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-lavtopsl/build.sh b/recipes/ucsc-lavtopsl/build.sh index 6bc1639458228..f3bad35b19a90 100644 --- a/recipes/ucsc-lavtopsl/build.sh +++ b/recipes/ucsc-lavtopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/lavToPsl && make) -cp bin/lavToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/lavToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/lavToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/lavToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/lavToPsl" diff --git a/recipes/ucsc-lavtopsl/include.patch b/recipes/ucsc-lavtopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-lavtopsl/include.patch +++ b/recipes/ucsc-lavtopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-lavtopsl/meta.yaml b/recipes/ucsc-lavtopsl/meta.yaml index e561090f1335f..cfc2c04b24fa7 100644 --- a/recipes/ucsc-lavtopsl/meta.yaml +++ b/recipes/ucsc-lavtopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-lavtopsl" %} {% set program = "lavToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert blastz lav to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ldhggene/build.sh b/recipes/ucsc-ldhggene/build.sh index f03594d189cf0..bcfee33c689a7 100644 --- a/recipes/ucsc-ldhggene/build.sh +++ b/recipes/ucsc-ldhggene/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/makeDb/ldHgGene && make) -cp bin/ldHgGene "$PREFIX/bin" -chmod +x "$PREFIX/bin/ldHgGene" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/makeDb/ldHgGene && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/ldHgGene "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/ldHgGene" diff --git a/recipes/ucsc-ldhggene/include.patch b/recipes/ucsc-ldhggene/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ldhggene/include.patch +++ b/recipes/ucsc-ldhggene/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ldhggene/meta.yaml b/recipes/ucsc-ldhggene/meta.yaml index 629f7cfa8254a..7efd6865ba331 100644 --- a/recipes/ucsc-ldhggene/meta.yaml +++ b/recipes/ucsc-ldhggene/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ldhggene" %} {% set program = "ldHgGene" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "load database with gene predictions from a gff file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-liftover/build.sh b/recipes/ucsc-liftover/build.sh index 189c409009472..50f0e8474db9a 100644 --- a/recipes/ucsc-liftover/build.sh +++ b/recipes/ucsc-liftover/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j${CPU_COUNT}) -(cd kent/src/htslib && make -j${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j${CPU_COUNT}) -(cd kent/src/hg/lib && make -j${CPU_COUNT}) -(cd kent/src/hg/liftOver && make -j${CPU_COUNT}) -cp bin/liftOver "$PREFIX/bin" -chmod +x "$PREFIX/bin/liftOver" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/liftOver && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/liftOver "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/liftOver" diff --git a/recipes/ucsc-liftover/include.patch b/recipes/ucsc-liftover/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-liftover/include.patch +++ b/recipes/ucsc-liftover/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-liftover/meta.yaml b/recipes/ucsc-liftover/meta.yaml index 4d953bf48e005..35cb3b9bb7a61 100644 --- a/recipes/ucsc-liftover/meta.yaml +++ b/recipes/ucsc-liftover/meta.yaml @@ -1,25 +1,21 @@ {% set package = "ucsc-liftover" %} {% set program = "liftOver" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 1 - skip: True # [osx] - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Move annotations from one assembly to another" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-liftup/build.sh b/recipes/ucsc-liftup/build.sh index 5a638019c0676..1a14a6cb069d0 100644 --- a/recipes/ucsc-liftup/build.sh +++ b/recipes/ucsc-liftup/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/liftUp && make) -cp bin/liftUp "$PREFIX/bin" -chmod +x "$PREFIX/bin/liftUp" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/liftUp && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/liftUp "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/liftUp" diff --git a/recipes/ucsc-liftup/include.patch b/recipes/ucsc-liftup/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-liftup/include.patch +++ b/recipes/ucsc-liftup/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-liftup/meta.yaml b/recipes/ucsc-liftup/meta.yaml index 87acba1d33d82..2de7a9e35a8d6 100644 --- a/recipes/ucsc-liftup/meta.yaml +++ b/recipes/ucsc-liftup/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-liftup" %} {% set program = "liftUp" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-linestora/build.sh b/recipes/ucsc-linestora/build.sh index 945e02d5d447d..eb58c0fc0db43 100644 --- a/recipes/ucsc-linestora/build.sh +++ b/recipes/ucsc-linestora/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raToLines/linesToRa && make) -cp bin/linesToRa "$PREFIX/bin" -chmod +x "$PREFIX/bin/linesToRa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/raToLines/linesToRa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/linesToRa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/linesToRa" diff --git a/recipes/ucsc-linestora/include.patch b/recipes/ucsc-linestora/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-linestora/include.patch +++ b/recipes/ucsc-linestora/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-linestora/meta.yaml b/recipes/ucsc-linestora/meta.yaml index 58fd0d3a47e68..8929fdad5aeff 100644 --- a/recipes/ucsc-linestora/meta.yaml +++ b/recipes/ucsc-linestora/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-linestora" %} {% set program = "linesToRa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "generate .ra format from lines with pipe-separated fields" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-localtime/build.sh b/recipes/ucsc-localtime/build.sh index 5e4271dc0c297..b0b32fe905438 100644 --- a/recipes/ucsc-localtime/build.sh +++ b/recipes/ucsc-localtime/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/timing/localtime && make) -cp bin/localtime "$PREFIX/bin" -chmod +x "$PREFIX/bin/localtime" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/timing/localtime && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/localtime "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/localtime" diff --git a/recipes/ucsc-localtime/include.patch b/recipes/ucsc-localtime/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-localtime/include.patch +++ b/recipes/ucsc-localtime/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-localtime/meta.yaml b/recipes/ucsc-localtime/meta.yaml index fe6a48b0afb65..9a5bb720eea6a 100644 --- a/recipes/ucsc-localtime/meta.yaml +++ b/recipes/ucsc-localtime/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-localtime" %} {% set program = "localtime" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert unix timestamp to date string" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafaddirows/build.sh b/recipes/ucsc-mafaddirows/build.sh index e7d550df0494d..cac297e03b3d9 100644 --- a/recipes/ucsc-mafaddirows/build.sh +++ b/recipes/ucsc-mafaddirows/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafAddIRows && make) -cp bin/mafAddIRows "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafAddIRows" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafAddIRows && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafAddIRows "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafAddIRows" diff --git a/recipes/ucsc-mafaddirows/include.patch b/recipes/ucsc-mafaddirows/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafaddirows/include.patch +++ b/recipes/ucsc-mafaddirows/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafaddirows/meta.yaml b/recipes/ucsc-mafaddirows/meta.yaml index 5d99df62b05d9..1678cf8b45d74 100644 --- a/recipes/ucsc-mafaddirows/meta.yaml +++ b/recipes/ucsc-mafaddirows/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafaddirows" %} {% set program = "mafAddIRows" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "add 'i' rows to a maf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafaddqrows/build.sh b/recipes/ucsc-mafaddqrows/build.sh index 2a500dafaef18..ed596762c367a 100644 --- a/recipes/ucsc-mafaddqrows/build.sh +++ b/recipes/ucsc-mafaddqrows/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafAddQRows && make) -cp bin/mafAddQRows "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafAddQRows" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafAddQRows && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafAddQRows "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafAddQRows" diff --git a/recipes/ucsc-mafaddqrows/include.patch b/recipes/ucsc-mafaddqrows/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafaddqrows/include.patch +++ b/recipes/ucsc-mafaddqrows/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafaddqrows/meta.yaml b/recipes/ucsc-mafaddqrows/meta.yaml index f9017087a7315..852353ae2d074 100644 --- a/recipes/ucsc-mafaddqrows/meta.yaml +++ b/recipes/ucsc-mafaddqrows/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafaddqrows" %} {% set program = "mafAddQRows" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add quality data to a maf" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafcoverage/build.sh b/recipes/ucsc-mafcoverage/build.sh index 348d70bc50d75..468207ac0d869 100644 --- a/recipes/ucsc-mafcoverage/build.sh +++ b/recipes/ucsc-mafcoverage/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafCoverage && make) -cp bin/mafCoverage "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafCoverage" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafCoverage && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafCoverage "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafCoverage" diff --git a/recipes/ucsc-mafcoverage/include.patch b/recipes/ucsc-mafcoverage/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafcoverage/include.patch +++ b/recipes/ucsc-mafcoverage/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafcoverage/meta.yaml b/recipes/ucsc-mafcoverage/meta.yaml index 098e92ad735b5..8e44dad771940 100644 --- a/recipes/ucsc-mafcoverage/meta.yaml +++ b/recipes/ucsc-mafcoverage/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafcoverage" %} {% set program = "mafCoverage" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Analyse coverage by maf files - chromosome by " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maffetch/build.sh b/recipes/ucsc-maffetch/build.sh index 645c5ada6b7fd..05845f691ae3f 100644 --- a/recipes/ucsc-maffetch/build.sh +++ b/recipes/ucsc-maffetch/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafFetch && make) -cp bin/mafFetch "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFetch" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafFetch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFetch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFetch" diff --git a/recipes/ucsc-maffetch/include.patch b/recipes/ucsc-maffetch/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffetch/include.patch +++ b/recipes/ucsc-maffetch/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffetch/meta.yaml b/recipes/ucsc-maffetch/meta.yaml index 0bcc9b3c66e88..9e20053386223 100644 --- a/recipes/ucsc-maffetch/meta.yaml +++ b/recipes/ucsc-maffetch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffetch" %} {% set program = "mafFetch" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get overlapping records from an MAF using an index table" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maffilter/build.sh b/recipes/ucsc-maffilter/build.sh index 1456dd4eba626..9843b09843d39 100644 --- a/recipes/ucsc-maffilter/build.sh +++ b/recipes/ucsc-maffilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafFilter && make) -cp bin/mafFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFilter" diff --git a/recipes/ucsc-maffilter/include.patch b/recipes/ucsc-maffilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffilter/include.patch +++ b/recipes/ucsc-maffilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffilter/meta.yaml b/recipes/ucsc-maffilter/meta.yaml index 7663b1c8a008c..fe2bdf5d06413 100644 --- a/recipes/ucsc-maffilter/meta.yaml +++ b/recipes/ucsc-maffilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffilter" %} {% set program = "mafFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter out maf files. Output goes to standard out" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maffrag/build.sh b/recipes/ucsc-maffrag/build.sh index f2386fc8ed4df..d9960af580f54 100644 --- a/recipes/ucsc-maffrag/build.sh +++ b/recipes/ucsc-maffrag/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafFrag && make) -cp bin/mafFrag "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFrag" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafFrag && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFrag "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFrag" diff --git a/recipes/ucsc-maffrag/include.patch b/recipes/ucsc-maffrag/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffrag/include.patch +++ b/recipes/ucsc-maffrag/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffrag/meta.yaml b/recipes/ucsc-maffrag/meta.yaml index f65ce536626f5..cd138bb8ded8a 100644 --- a/recipes/ucsc-maffrag/meta.yaml +++ b/recipes/ucsc-maffrag/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffrag" %} {% set program = "mafFrag" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract maf sequences for a region from database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maffrags/build.sh b/recipes/ucsc-maffrags/build.sh index b058c5853bc14..1e18fa9821f72 100644 --- a/recipes/ucsc-maffrags/build.sh +++ b/recipes/ucsc-maffrags/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafFrags && make) -cp bin/mafFrags "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafFrags" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafFrags && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafFrags "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafFrags" diff --git a/recipes/ucsc-maffrags/include.patch b/recipes/ucsc-maffrags/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maffrags/include.patch +++ b/recipes/ucsc-maffrags/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maffrags/meta.yaml b/recipes/ucsc-maffrags/meta.yaml index 21cd93f53f83e..37d1e5f3345ea 100644 --- a/recipes/ucsc-maffrags/meta.yaml +++ b/recipes/ucsc-maffrags/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maffrags" %} {% set program = "mafFrags" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Collect MAFs from regions specified in a 6 column bed file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafgene/build.sh b/recipes/ucsc-mafgene/build.sh index 6ef25dbca5c93..b3fd8c73fa645 100644 --- a/recipes/ucsc-mafgene/build.sh +++ b/recipes/ucsc-mafgene/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafGene && make) -cp bin/mafGene "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafGene" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafGene && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafGene "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafGene" diff --git a/recipes/ucsc-mafgene/include.patch b/recipes/ucsc-mafgene/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafgene/include.patch +++ b/recipes/ucsc-mafgene/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafgene/meta.yaml b/recipes/ucsc-mafgene/meta.yaml index 9912fd7602673..b7e0f85af8626 100644 --- a/recipes/ucsc-mafgene/meta.yaml +++ b/recipes/ucsc-mafgene/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafgene" %} {% set program = "mafGene" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "output protein alignments using maf and genePred" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafmefirst/build.sh b/recipes/ucsc-mafmefirst/build.sh index 4363fc2b59ba9..6ffa033237548 100644 --- a/recipes/ucsc-mafmefirst/build.sh +++ b/recipes/ucsc-mafmefirst/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafMeFirst && make) -cp bin/mafMeFirst "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafMeFirst" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafMeFirst && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafMeFirst "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafMeFirst" diff --git a/recipes/ucsc-mafmefirst/include.patch b/recipes/ucsc-mafmefirst/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafmefirst/include.patch +++ b/recipes/ucsc-mafmefirst/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafmefirst/meta.yaml b/recipes/ucsc-mafmefirst/meta.yaml index e48007351af53..4ee6e4b03ce1e 100644 --- a/recipes/ucsc-mafmefirst/meta.yaml +++ b/recipes/ucsc-mafmefirst/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafmefirst" %} {% set program = "mafMeFirst" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Move component to top if it is one of the named ones. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maforder/build.sh b/recipes/ucsc-maforder/build.sh index cefff99c5bdf1..a89bd8868c424 100644 --- a/recipes/ucsc-maforder/build.sh +++ b/recipes/ucsc-maforder/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafOrder && make) -cp bin/mafOrder "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafOrder" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafOrder && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafOrder "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafOrder" diff --git a/recipes/ucsc-maforder/include.patch b/recipes/ucsc-maforder/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maforder/include.patch +++ b/recipes/ucsc-maforder/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maforder/meta.yaml b/recipes/ucsc-maforder/meta.yaml index 54bfd559eb179..ad84eab22d85c 100644 --- a/recipes/ucsc-maforder/meta.yaml +++ b/recipes/ucsc-maforder/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maforder" %} {% set program = "mafOrder" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "order components within a maf file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafranges/build.sh b/recipes/ucsc-mafranges/build.sh index 0441760e4d982..e1687873c6d65 100644 --- a/recipes/ucsc-mafranges/build.sh +++ b/recipes/ucsc-mafranges/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafRanges && make) -cp bin/mafRanges "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafRanges" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafRanges && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafRanges "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafRanges" diff --git a/recipes/ucsc-mafranges/include.patch b/recipes/ucsc-mafranges/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafranges/include.patch +++ b/recipes/ucsc-mafranges/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafranges/meta.yaml b/recipes/ucsc-mafranges/meta.yaml index 6510d41b8bb8e..66d3c977d9dc7 100644 --- a/recipes/ucsc-mafranges/meta.yaml +++ b/recipes/ucsc-mafranges/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafranges" %} {% set program = "mafRanges" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract ranges of target (or query) coverage from maf and " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafsinregion/build.sh b/recipes/ucsc-mafsinregion/build.sh index 3e8ea07de6c37..4fb3f28a5e560 100644 --- a/recipes/ucsc-mafsinregion/build.sh +++ b/recipes/ucsc-mafsinregion/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafsInRegion && make) -cp bin/mafsInRegion "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafsInRegion" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafsInRegion && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafsInRegion "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafsInRegion" diff --git a/recipes/ucsc-mafsinregion/include.patch b/recipes/ucsc-mafsinregion/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafsinregion/include.patch +++ b/recipes/ucsc-mafsinregion/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafsinregion/meta.yaml b/recipes/ucsc-mafsinregion/meta.yaml index 81d418c4524e2..48415aa8bb4dc 100644 --- a/recipes/ucsc-mafsinregion/meta.yaml +++ b/recipes/ucsc-mafsinregion/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafsinregion" %} {% set program = "mafsInRegion" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract MAFS in a genomic region" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafspecieslist/build.sh b/recipes/ucsc-mafspecieslist/build.sh index fb5f2c9fc419c..b55e48756c1d1 100644 --- a/recipes/ucsc-mafspecieslist/build.sh +++ b/recipes/ucsc-mafspecieslist/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSpeciesList && make) -cp bin/mafSpeciesList "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSpeciesList" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSpeciesList && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSpeciesList "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSpeciesList" diff --git a/recipes/ucsc-mafspecieslist/include.patch b/recipes/ucsc-mafspecieslist/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafspecieslist/include.patch +++ b/recipes/ucsc-mafspecieslist/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafspecieslist/meta.yaml b/recipes/ucsc-mafspecieslist/meta.yaml index db844606494ed..39fea6c3f3bcf 100644 --- a/recipes/ucsc-mafspecieslist/meta.yaml +++ b/recipes/ucsc-mafspecieslist/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafspecieslist" %} {% set program = "mafSpeciesList" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Scan maf and output all species used in it." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafspeciessubset/build.sh b/recipes/ucsc-mafspeciessubset/build.sh index 57941b4e15733..f1c3303a4e9d3 100644 --- a/recipes/ucsc-mafspeciessubset/build.sh +++ b/recipes/ucsc-mafspeciessubset/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSpeciesSubset && make) -cp bin/mafSpeciesSubset "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSpeciesSubset" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSpeciesSubset && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSpeciesSubset "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSpeciesSubset" diff --git a/recipes/ucsc-mafspeciessubset/include.patch b/recipes/ucsc-mafspeciessubset/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafspeciessubset/include.patch +++ b/recipes/ucsc-mafspeciessubset/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafspeciessubset/meta.yaml b/recipes/ucsc-mafspeciessubset/meta.yaml index 29994a6b0c59f..566864c8adf9a 100644 --- a/recipes/ucsc-mafspeciessubset/meta.yaml +++ b/recipes/ucsc-mafspeciessubset/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafspeciessubset" %} {% set program = "mafSpeciesSubset" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract a maf that just has a subset of species." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafsplit/build.sh b/recipes/ucsc-mafsplit/build.sh index 16a94db036ce9..c95e8038cb565 100644 --- a/recipes/ucsc-mafsplit/build.sh +++ b/recipes/ucsc-mafsplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSplit && make) -cp bin/mafSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSplit" diff --git a/recipes/ucsc-mafsplit/include.patch b/recipes/ucsc-mafsplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafsplit/include.patch +++ b/recipes/ucsc-mafsplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafsplit/meta.yaml b/recipes/ucsc-mafsplit/meta.yaml index 57c217ce78e8b..8fb771c78e0c5 100644 --- a/recipes/ucsc-mafsplit/meta.yaml +++ b/recipes/ucsc-mafsplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafsplit" %} {% set program = "mafSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split multiple alignment files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mafsplitpos/build.sh b/recipes/ucsc-mafsplitpos/build.sh index 3c410b8870dc6..755b371f59363 100644 --- a/recipes/ucsc-mafsplitpos/build.sh +++ b/recipes/ucsc-mafsplitpos/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafSplitPos && make) -cp bin/mafSplitPos "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafSplitPos" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafSplitPos && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafSplitPos "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafSplitPos" diff --git a/recipes/ucsc-mafsplitpos/include.patch b/recipes/ucsc-mafsplitpos/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mafsplitpos/include.patch +++ b/recipes/ucsc-mafsplitpos/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mafsplitpos/meta.yaml b/recipes/ucsc-mafsplitpos/meta.yaml index 8c0fb2d4ad59c..e0217c186b004 100644 --- a/recipes/ucsc-mafsplitpos/meta.yaml +++ b/recipes/ucsc-mafsplitpos/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mafsplitpos" %} {% set program = "mafSplitPos" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Pick positions to split multiple alignment input files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftoaxt/build.sh b/recipes/ucsc-maftoaxt/build.sh index d1c547e94566a..915b30b593cce 100644 --- a/recipes/ucsc-maftoaxt/build.sh +++ b/recipes/ucsc-maftoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafToAxt && make) -cp bin/mafToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToAxt" diff --git a/recipes/ucsc-maftoaxt/include.patch b/recipes/ucsc-maftoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftoaxt/include.patch +++ b/recipes/ucsc-maftoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftoaxt/meta.yaml b/recipes/ucsc-maftoaxt/meta.yaml index 30844b9a378a5..2e31d3a08bf55 100644 --- a/recipes/ucsc-maftoaxt/meta.yaml +++ b/recipes/ucsc-maftoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftoaxt" %} {% set program = "mafToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from maf to axt format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftobigmaf/build.sh b/recipes/ucsc-maftobigmaf/build.sh index b8f624f13c557..9e78fbddae397 100644 --- a/recipes/ucsc-maftobigmaf/build.sh +++ b/recipes/ucsc-maftobigmaf/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/mafToBigMaf && make) -cp bin/mafToBigMaf "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToBigMaf" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/mafToBigMaf && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToBigMaf "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToBigMaf" diff --git a/recipes/ucsc-maftobigmaf/include.patch b/recipes/ucsc-maftobigmaf/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftobigmaf/include.patch +++ b/recipes/ucsc-maftobigmaf/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftobigmaf/meta.yaml b/recipes/ucsc-maftobigmaf/meta.yaml index 823170338eb05..e99a1f9fec06f 100644 --- a/recipes/ucsc-maftobigmaf/meta.yaml +++ b/recipes/ucsc-maftobigmaf/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftobigmaf" %} {% set program = "mafToBigMaf" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Put ucsc standard maf file into bigMaf format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftopsl/build.sh b/recipes/ucsc-maftopsl/build.sh index c9de71f45a5ed..3889b11a30b41 100644 --- a/recipes/ucsc-maftopsl/build.sh +++ b/recipes/ucsc-maftopsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/mafToPsl && make) -cp bin/mafToPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/mafToPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToPsl" diff --git a/recipes/ucsc-maftopsl/include.patch b/recipes/ucsc-maftopsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftopsl/include.patch +++ b/recipes/ucsc-maftopsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftopsl/meta.yaml b/recipes/ucsc-maftopsl/meta.yaml index b47c1683b1e3b..ede1d2177c11c 100644 --- a/recipes/ucsc-maftopsl/meta.yaml +++ b/recipes/ucsc-maftopsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftopsl" %} {% set program = "mafToPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert maf to psl format" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maftosnpbed/build.sh b/recipes/ucsc-maftosnpbed/build.sh index d85e46296e96a..50318d5b9132e 100644 --- a/recipes/ucsc-maftosnpbed/build.sh +++ b/recipes/ucsc-maftosnpbed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/ratStuff/mafToSnpBed && make) -cp bin/mafToSnpBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/mafToSnpBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/ratStuff/mafToSnpBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mafToSnpBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mafToSnpBed" diff --git a/recipes/ucsc-maftosnpbed/include.patch b/recipes/ucsc-maftosnpbed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maftosnpbed/include.patch +++ b/recipes/ucsc-maftosnpbed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maftosnpbed/meta.yaml b/recipes/ucsc-maftosnpbed/meta.yaml index ec50b9371c946..b394aaa8ed1ce 100644 --- a/recipes/ucsc-maftosnpbed/meta.yaml +++ b/recipes/ucsc-maftosnpbed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maftosnpbed" %} {% set program = "mafToSnpBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "finds SNPs in MAF and builds a bed with their functional consequence" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maketablelist/build.sh b/recipes/ucsc-maketablelist/build.sh index 5511e7edf2d17..637891a953eb6 100644 --- a/recipes/ucsc-maketablelist/build.sh +++ b/recipes/ucsc-maketablelist/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/makeTableList && make) -cp bin/makeTableList "$PREFIX/bin" -chmod +x "$PREFIX/bin/makeTableList" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/makeTableList && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/makeTableList "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/makeTableList" diff --git a/recipes/ucsc-maketablelist/include.patch b/recipes/ucsc-maketablelist/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maketablelist/include.patch +++ b/recipes/ucsc-maketablelist/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maketablelist/meta.yaml b/recipes/ucsc-maketablelist/meta.yaml index bed1d94da6a3d..484f0b4420f86 100644 --- a/recipes/ucsc-maketablelist/meta.yaml +++ b/recipes/ucsc-maketablelist/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maketablelist" %} {% set program = "makeTableList" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-maskoutfa/build.sh b/recipes/ucsc-maskoutfa/build.sh index 2f24ecb8fe45d..27e2043807128 100644 --- a/recipes/ucsc-maskoutfa/build.sh +++ b/recipes/ucsc-maskoutfa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/maskOutFa && make) -cp bin/maskOutFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/maskOutFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/maskOutFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/maskOutFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/maskOutFa" diff --git a/recipes/ucsc-maskoutfa/include.patch b/recipes/ucsc-maskoutfa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-maskoutfa/include.patch +++ b/recipes/ucsc-maskoutfa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-maskoutfa/meta.yaml b/recipes/ucsc-maskoutfa/meta.yaml index 9edb65eb58987..fa8cc7eb1593a 100644 --- a/recipes/ucsc-maskoutfa/meta.yaml +++ b/recipes/ucsc-maskoutfa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-maskoutfa" %} {% set program = "maskOutFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Produce a masked .fa file given an unmasked .fa and" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mktime/build.sh b/recipes/ucsc-mktime/build.sh index ac60435474cef..736038679a3b1 100644 --- a/recipes/ucsc-mktime/build.sh +++ b/recipes/ucsc-mktime/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/timing/mktime && make) -cp bin/mktime "$PREFIX/bin" -chmod +x "$PREFIX/bin/mktime" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/timing/mktime && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mktime "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mktime" diff --git a/recipes/ucsc-mktime/include.patch b/recipes/ucsc-mktime/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mktime/include.patch +++ b/recipes/ucsc-mktime/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mktime/meta.yaml b/recipes/ucsc-mktime/meta.yaml index ff8b7b04ca583..e52b1b0b0c71b 100644 --- a/recipes/ucsc-mktime/meta.yaml +++ b/recipes/ucsc-mktime/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mktime" %} {% set program = "mktime" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert date string to unix timestamp" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-mrnatogene/build.sh b/recipes/ucsc-mrnatogene/build.sh index 1f51dc89ac019..356d27d294304 100644 --- a/recipes/ucsc-mrnatogene/build.sh +++ b/recipes/ucsc-mrnatogene/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mrnaToGene && make) -cp bin/mrnaToGene "$PREFIX/bin" -chmod +x "$PREFIX/bin/mrnaToGene" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mrnaToGene && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/mrnaToGene "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/mrnaToGene" diff --git a/recipes/ucsc-mrnatogene/include.patch b/recipes/ucsc-mrnatogene/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-mrnatogene/include.patch +++ b/recipes/ucsc-mrnatogene/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-mrnatogene/meta.yaml b/recipes/ucsc-mrnatogene/meta.yaml index d20f36281b5ff..ce964281b2d9c 100644 --- a/recipes/ucsc-mrnatogene/meta.yaml +++ b/recipes/ucsc-mrnatogene/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-mrnatogene" %} {% set program = "mrnaToGene" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert PSL alignments of mRNAs to gene annotations" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netchainsubset/build.sh b/recipes/ucsc-netchainsubset/build.sh index 8427193703407..59ab5b713497e 100644 --- a/recipes/ucsc-netchainsubset/build.sh +++ b/recipes/ucsc-netchainsubset/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netChainSubset && make) -cp bin/netChainSubset "$PREFIX/bin" -chmod +x "$PREFIX/bin/netChainSubset" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netChainSubset && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netChainSubset "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netChainSubset" diff --git a/recipes/ucsc-netchainsubset/include.patch b/recipes/ucsc-netchainsubset/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netchainsubset/include.patch +++ b/recipes/ucsc-netchainsubset/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netchainsubset/meta.yaml b/recipes/ucsc-netchainsubset/meta.yaml index d877f1327402a..2f921aa504a60 100644 --- a/recipes/ucsc-netchainsubset/meta.yaml +++ b/recipes/ucsc-netchainsubset/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netchainsubset" %} {% set program = "netChainSubset" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Create chain file with subset of chains that appear in the net" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netclass/build.sh b/recipes/ucsc-netclass/build.sh index 68e9b089f5bcb..cf06d9c6b23c1 100644 --- a/recipes/ucsc-netclass/build.sh +++ b/recipes/ucsc-netclass/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netClass && make) -cp bin/netClass "$PREFIX/bin" -chmod +x "$PREFIX/bin/netClass" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netClass && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netClass "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netClass" diff --git a/recipes/ucsc-netclass/include.patch b/recipes/ucsc-netclass/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netclass/include.patch +++ b/recipes/ucsc-netclass/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netclass/meta.yaml b/recipes/ucsc-netclass/meta.yaml index 48be742bee886..921a2ffc48eaf 100644 --- a/recipes/ucsc-netclass/meta.yaml +++ b/recipes/ucsc-netclass/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netclass" %} {% set program = "netClass" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add classification info to net" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netfilter/build.sh b/recipes/ucsc-netfilter/build.sh index be78f3e060ccc..69dd249c8e00d 100644 --- a/recipes/ucsc-netfilter/build.sh +++ b/recipes/ucsc-netfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netFilter && make) -cp bin/netFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/netFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netFilter" diff --git a/recipes/ucsc-netfilter/include.patch b/recipes/ucsc-netfilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netfilter/include.patch +++ b/recipes/ucsc-netfilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netfilter/meta.yaml b/recipes/ucsc-netfilter/meta.yaml index 0561f41a51fc9..59415265530ab 100644 --- a/recipes/ucsc-netfilter/meta.yaml +++ b/recipes/ucsc-netfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netfilter" %} {% set program = "netFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Filter out parts of net. What passes" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netsplit/build.sh b/recipes/ucsc-netsplit/build.sh index 75be84d8d69e7..5baa0ef4281d0 100644 --- a/recipes/ucsc-netsplit/build.sh +++ b/recipes/ucsc-netsplit/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netSplit && make) -cp bin/netSplit "$PREFIX/bin" -chmod +x "$PREFIX/bin/netSplit" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netSplit && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netSplit "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netSplit" diff --git a/recipes/ucsc-netsplit/include.patch b/recipes/ucsc-netsplit/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netsplit/include.patch +++ b/recipes/ucsc-netsplit/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netsplit/meta.yaml b/recipes/ucsc-netsplit/meta.yaml index 8c6739a77a8e9..feca545a7efbc 100644 --- a/recipes/ucsc-netsplit/meta.yaml +++ b/recipes/ucsc-netsplit/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netsplit" %} {% set program = "netSplit" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split a genome net file into chromosome net files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-netsyntenic/build.sh b/recipes/ucsc-netsyntenic/build.sh index 2ac9ac5182941..5e8aebf053581 100644 --- a/recipes/ucsc-netsyntenic/build.sh +++ b/recipes/ucsc-netsyntenic/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netSyntenic && make) -cp bin/netSyntenic "$PREFIX/bin" -chmod +x "$PREFIX/bin/netSyntenic" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netSyntenic && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netSyntenic "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netSyntenic" diff --git a/recipes/ucsc-netsyntenic/include.patch b/recipes/ucsc-netsyntenic/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-netsyntenic/include.patch +++ b/recipes/ucsc-netsyntenic/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-netsyntenic/meta.yaml b/recipes/ucsc-netsyntenic/meta.yaml index 81b2bddddd265..87b26bea97f27 100644 --- a/recipes/ucsc-netsyntenic/meta.yaml +++ b/recipes/ucsc-netsyntenic/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-netsyntenic" %} {% set program = "netSyntenic" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Add synteny info to net." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-nettoaxt/build.sh b/recipes/ucsc-nettoaxt/build.sh index 733eca3ea04bf..73bdfb3fd65e8 100644 --- a/recipes/ucsc-nettoaxt/build.sh +++ b/recipes/ucsc-nettoaxt/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netToAxt && make) -cp bin/netToAxt "$PREFIX/bin" -chmod +x "$PREFIX/bin/netToAxt" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netToAxt && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netToAxt "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netToAxt" diff --git a/recipes/ucsc-nettoaxt/include.patch b/recipes/ucsc-nettoaxt/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-nettoaxt/include.patch +++ b/recipes/ucsc-nettoaxt/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-nettoaxt/meta.yaml b/recipes/ucsc-nettoaxt/meta.yaml index 52f7b5123312b..aeef00d707002 100644 --- a/recipes/ucsc-nettoaxt/meta.yaml +++ b/recipes/ucsc-nettoaxt/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nettoaxt" %} {% set program = "netToAxt" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert net (and chain) to axt." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-nettobed/build.sh b/recipes/ucsc-nettobed/build.sh index ebd0e971bcab6..f24f2ee9b350d 100644 --- a/recipes/ucsc-nettobed/build.sh +++ b/recipes/ucsc-nettobed/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/mouseStuff/netToBed && make) -cp bin/netToBed "$PREFIX/bin" -chmod +x "$PREFIX/bin/netToBed" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/mouseStuff/netToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/netToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/netToBed" diff --git a/recipes/ucsc-nettobed/include.patch b/recipes/ucsc-nettobed/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-nettobed/include.patch +++ b/recipes/ucsc-nettobed/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-nettobed/meta.yaml b/recipes/ucsc-nettobed/meta.yaml index a1278573aba66..78ef0cc414f73 100644 --- a/recipes/ucsc-nettobed/meta.yaml +++ b/recipes/ucsc-nettobed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nettobed" %} {% set program = "netToBed" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert target coverage of net to a bed file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-newprog/build.sh b/recipes/ucsc-newprog/build.sh index c3ae494488a4a..8549421304b91 100644 --- a/recipes/ucsc-newprog/build.sh +++ b/recipes/ucsc-newprog/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/newProg && make) -cp bin/newProg "$PREFIX/bin" -chmod +x "$PREFIX/bin/newProg" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/newProg && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/newProg "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/newProg" diff --git a/recipes/ucsc-newprog/include.patch b/recipes/ucsc-newprog/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-newprog/include.patch +++ b/recipes/ucsc-newprog/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-newprog/meta.yaml b/recipes/ucsc-newprog/meta.yaml index 9d93bc10fe5fe..4f06ccbc16664 100644 --- a/recipes/ucsc-newprog/meta.yaml +++ b/recipes/ucsc-newprog/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-newprog" %} {% set program = "newProg" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "make a new C source skeleton." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-newpythonprog/build.sh b/recipes/ucsc-newpythonprog/build.sh index a049d1734108b..9b3d10a8a6f99 100644 --- a/recipes/ucsc-newpythonprog/build.sh +++ b/recipes/ucsc-newpythonprog/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/newPythonProg && make) -cp bin/newPythonProg "$PREFIX/bin" -chmod +x "$PREFIX/bin/newPythonProg" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/newPythonProg && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/newPythonProg "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/newPythonProg" diff --git a/recipes/ucsc-newpythonprog/include.patch b/recipes/ucsc-newpythonprog/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-newpythonprog/include.patch +++ b/recipes/ucsc-newpythonprog/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-newpythonprog/meta.yaml b/recipes/ucsc-newpythonprog/meta.yaml index 7f8c05c0c5380..361d9f8b5f4fd 100644 --- a/recipes/ucsc-newpythonprog/meta.yaml +++ b/recipes/ucsc-newpythonprog/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-newpythonprog" %} {% set program = "newPythonProg" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make a skeleton for a new python program" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-nibfrag/build.sh b/recipes/ucsc-nibfrag/build.sh index 088a651a09043..bb08f993f9b15 100644 --- a/recipes/ucsc-nibfrag/build.sh +++ b/recipes/ucsc-nibfrag/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/nibFrag && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -x bin/nibFrag "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/nibFrag" +cp bin/nibFrag "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/nibFrag" diff --git a/recipes/ucsc-nibfrag/meta.yaml b/recipes/ucsc-nibfrag/meta.yaml index 17bb497cfb5d5..d62bed526b13b 100644 --- a/recipes/ucsc-nibfrag/meta.yaml +++ b/recipes/ucsc-nibfrag/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nibfrag" %} {% set program = "nibFrag" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract part of a nib file as .fa (all bases/gaps lower case by default)" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-nibsize/build.sh b/recipes/ucsc-nibsize/build.sh index e2caa29987ced..7a2721a2626ba 100644 --- a/recipes/ucsc-nibsize/build.sh +++ b/recipes/ucsc-nibsize/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/nibSize && make) -cp bin/nibSize "$PREFIX/bin" -chmod +x "$PREFIX/bin/nibSize" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/nibSize && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/nibSize "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/nibSize" diff --git a/recipes/ucsc-nibsize/include.patch b/recipes/ucsc-nibsize/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-nibsize/include.patch +++ b/recipes/ucsc-nibsize/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-nibsize/meta.yaml b/recipes/ucsc-nibsize/meta.yaml index 79d338775cab0..c137ff3bace8e 100644 --- a/recipes/ucsc-nibsize/meta.yaml +++ b/recipes/ucsc-nibsize/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-nibsize" %} {% set program = "nibSize" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "print size of nibs" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-oligomatch/build.sh b/recipes/ucsc-oligomatch/build.sh index a88ccff20a470..3d72e4bab8926 100644 --- a/recipes/ucsc-oligomatch/build.sh +++ b/recipes/ucsc-oligomatch/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/utils/oligoMatch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/oligoMatch "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/oligoMatch" +cp bin/oligoMatch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/oligoMatch" diff --git a/recipes/ucsc-oligomatch/meta.yaml b/recipes/ucsc-oligomatch/meta.yaml index e3e152c54dd21..f34d627ba9455 100644 --- a/recipes/ucsc-oligomatch/meta.yaml +++ b/recipes/ucsc-oligomatch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-oligomatch" %} {% set program = "oligoMatch" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "find perfect matches in sequence." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-overlapselect/build.sh b/recipes/ucsc-overlapselect/build.sh index cc2603b122258..142a3f3814a7c 100644 --- a/recipes/ucsc-overlapselect/build.sh +++ b/recipes/ucsc-overlapselect/build.sh @@ -1,15 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -export LIBRARY_PATH=$PREFIX/lib -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd kent/src/hg/utils/overlapSelect && make) -cp bin/overlapSelect "$PREFIX/bin" -chmod +x "$PREFIX/bin/overlapSelect" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/overlapSelect && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/overlapSelect "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/overlapSelect" diff --git a/recipes/ucsc-overlapselect/include.patch b/recipes/ucsc-overlapselect/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-overlapselect/include.patch +++ b/recipes/ucsc-overlapselect/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-overlapselect/meta.yaml b/recipes/ucsc-overlapselect/meta.yaml index c56ff504055c6..c299a79458e84 100644 --- a/recipes/ucsc-overlapselect/meta.yaml +++ b/recipes/ucsc-overlapselect/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-overlapselect" %} {% set program = "overlapSelect" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,24 +27,24 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. @@ -50,3 +52,12 @@ Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-para/build.sh b/recipes/ucsc-para/build.sh index 6fd859b06df5a..42637fdceedef 100644 --- a/recipes/ucsc-para/build.sh +++ b/recipes/ucsc-para/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/para "$PREFIX/bin" -chmod +x "$PREFIX/bin/para" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/para "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/para" diff --git a/recipes/ucsc-para/include.patch b/recipes/ucsc-para/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-para/include.patch +++ b/recipes/ucsc-para/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-para/meta.yaml b/recipes/ucsc-para/meta.yaml index ce4365c52b3fd..51ddc57dd7308 100644 --- a/recipes/ucsc-para/meta.yaml +++ b/recipes/ucsc-para/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-para" %} {% set program = "para" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parafetch/build.sh b/recipes/ucsc-parafetch/build.sh index 4ca0a8d0b0c96..4b721d3254311 100644 --- a/recipes/ucsc-parafetch/build.sh +++ b/recipes/ucsc-parafetch/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/paraFetch && make) -cp bin/paraFetch "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraFetch" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/paraFetch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/paraFetch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraFetch" diff --git a/recipes/ucsc-parafetch/include.patch b/recipes/ucsc-parafetch/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parafetch/include.patch +++ b/recipes/ucsc-parafetch/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parafetch/meta.yaml b/recipes/ucsc-parafetch/meta.yaml index f87780cd44f5a..027e9eb2c2a9f 100644 --- a/recipes/ucsc-parafetch/meta.yaml +++ b/recipes/ucsc-parafetch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parafetch" %} {% set program = "paraFetch" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "try to fetch url with multiple connections" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parahub/build.sh b/recipes/ucsc-parahub/build.sh index b07637d49880f..b3179ffe3b0ea 100644 --- a/recipes/ucsc-parahub/build.sh +++ b/recipes/ucsc-parahub/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraHub "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraHub" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraHub "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraHub" diff --git a/recipes/ucsc-parahub/include.patch b/recipes/ucsc-parahub/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parahub/include.patch +++ b/recipes/ucsc-parahub/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parahub/meta.yaml b/recipes/ucsc-parahub/meta.yaml index 1c6a1f5c685f9..5643cd381a146 100644 --- a/recipes/ucsc-parahub/meta.yaml +++ b/recipes/ucsc-parahub/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parahub" %} {% set program = "paraHub" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "parasol hub server version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parahubstop/build.sh b/recipes/ucsc-parahubstop/build.sh index b6d59daed3d1b..4928c38160983 100644 --- a/recipes/ucsc-parahubstop/build.sh +++ b/recipes/ucsc-parahubstop/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraHubStop "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraHubStop" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraHubStop "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraHubStop" diff --git a/recipes/ucsc-parahubstop/include.patch b/recipes/ucsc-parahubstop/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parahubstop/include.patch +++ b/recipes/ucsc-parahubstop/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parahubstop/meta.yaml b/recipes/ucsc-parahubstop/meta.yaml index 3db97dd0e5048..58351f6cdbfed 100644 --- a/recipes/ucsc-parahubstop/meta.yaml +++ b/recipes/ucsc-parahubstop/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parahubstop" %} {% set program = "paraHubStop" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranode/build.sh b/recipes/ucsc-paranode/build.sh index 9f0598370b27c..4264150ac6964 100644 --- a/recipes/ucsc-paranode/build.sh +++ b/recipes/ucsc-paranode/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNode "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNode" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNode "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNode" diff --git a/recipes/ucsc-paranode/include.patch b/recipes/ucsc-paranode/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranode/include.patch +++ b/recipes/ucsc-paranode/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranode/meta.yaml b/recipes/ucsc-paranode/meta.yaml index ac3724fcebfc6..bebf62ba576af 100644 --- a/recipes/ucsc-paranode/meta.yaml +++ b/recipes/ucsc-paranode/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranode" %} {% set program = "paraNode" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranodestart/build.sh b/recipes/ucsc-paranodestart/build.sh index 12c13b8de1cc0..bcd025dda9cfd 100644 --- a/recipes/ucsc-paranodestart/build.sh +++ b/recipes/ucsc-paranodestart/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNodeStart "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNodeStart" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNodeStart "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNodeStart" diff --git a/recipes/ucsc-paranodestart/include.patch b/recipes/ucsc-paranodestart/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranodestart/include.patch +++ b/recipes/ucsc-paranodestart/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranodestart/meta.yaml b/recipes/ucsc-paranodestart/meta.yaml index 616f68ffa2dc6..fc403349abe12 100644 --- a/recipes/ucsc-paranodestart/meta.yaml +++ b/recipes/ucsc-paranodestart/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranodestart" %} {% set program = "paraNodeStart" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranodestatus/build.sh b/recipes/ucsc-paranodestatus/build.sh index 1bcf47aaa7b35..511f3623d3dff 100644 --- a/recipes/ucsc-paranodestatus/build.sh +++ b/recipes/ucsc-paranodestatus/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNodeStatus "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNodeStatus" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNodeStatus "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNodeStatus" diff --git a/recipes/ucsc-paranodestatus/include.patch b/recipes/ucsc-paranodestatus/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranodestatus/include.patch +++ b/recipes/ucsc-paranodestatus/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranodestatus/meta.yaml b/recipes/ucsc-paranodestatus/meta.yaml index de880fd0e1e19..8f02ac48eb5c0 100644 --- a/recipes/ucsc-paranodestatus/meta.yaml +++ b/recipes/ucsc-paranodestatus/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranodestatus" %} {% set program = "paraNodeStatus" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paranodestop/build.sh b/recipes/ucsc-paranodestop/build.sh index 70ee91dcb5ccb..3bf8a31b65e09 100644 --- a/recipes/ucsc-paranodestop/build.sh +++ b/recipes/ucsc-paranodestop/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraNodeStop "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraNodeStop" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraNodeStop "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraNodeStop" diff --git a/recipes/ucsc-paranodestop/include.patch b/recipes/ucsc-paranodestop/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paranodestop/include.patch +++ b/recipes/ucsc-paranodestop/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paranodestop/meta.yaml b/recipes/ucsc-paranodestop/meta.yaml index 4cd1915969163..f7128debc7d61 100644 --- a/recipes/ucsc-paranodestop/meta.yaml +++ b/recipes/ucsc-paranodestop/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paranodestop" %} {% set program = "paraNodeStop" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,24 +27,33 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Shut down parasol node daemons on a list of machines " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parasol/build.sh b/recipes/ucsc-parasol/build.sh index 71cb7156a637c..0c8cf86fdf1eb 100644 --- a/recipes/ucsc-parasol/build.sh +++ b/recipes/ucsc-parasol/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/parasol "$PREFIX/bin" -chmod +x "$PREFIX/bin/parasol" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/parasol "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/parasol" diff --git a/recipes/ucsc-parasol/include.patch b/recipes/ucsc-parasol/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parasol/include.patch +++ b/recipes/ucsc-parasol/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parasol/meta.yaml b/recipes/ucsc-parasol/meta.yaml index 312af4a41ac72..0b01fffa4b53f 100644 --- a/recipes/ucsc-parasol/meta.yaml +++ b/recipes/ucsc-parasol/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parasol" %} {% set program = "parasol" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,27 +27,36 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-parasync/build.sh b/recipes/ucsc-parasync/build.sh index 471e37fc9c924..5d4414af87ee1 100644 --- a/recipes/ucsc-parasync/build.sh +++ b/recipes/ucsc-parasync/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/paraSync && make) -cp bin/paraSync "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraSync" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/paraSync && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/paraSync "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraSync" diff --git a/recipes/ucsc-parasync/include.patch b/recipes/ucsc-parasync/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-parasync/include.patch +++ b/recipes/ucsc-parasync/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-parasync/meta.yaml b/recipes/ucsc-parasync/meta.yaml index cd3b79f2d8324..ef74648b0d782 100644 --- a/recipes/ucsc-parasync/meta.yaml +++ b/recipes/ucsc-parasync/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-parasync" %} {% set program = "paraSync" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "uses paraFetch to recursively mirror url to given path" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-paratestjob/build.sh b/recipes/ucsc-paratestjob/build.sh index 3578cd03ac885..23d28f563e267 100644 --- a/recipes/ucsc-paratestjob/build.sh +++ b/recipes/ucsc-paratestjob/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/parasol && make) -cp kent/src/parasol/bin/paraTestJob "$PREFIX/bin" -chmod +x "$PREFIX/bin/paraTestJob" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/parasol && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp kent/src/parasol/bin/paraTestJob "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/paraTestJob" diff --git a/recipes/ucsc-paratestjob/include.patch b/recipes/ucsc-paratestjob/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-paratestjob/include.patch +++ b/recipes/ucsc-paratestjob/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-paratestjob/meta.yaml b/recipes/ucsc-paratestjob/meta.yaml index ab5b4396c8617..edbd7f5781f3d 100644 --- a/recipes/ucsc-paratestjob/meta.yaml +++ b/recipes/ucsc-paratestjob/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-paratestjob" %} {% set program = "paraTestJob" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "version 12.18" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-positionaltblcheck/build.sh b/recipes/ucsc-positionaltblcheck/build.sh index 2aac0fb259542..4a2db6d3472b3 100644 --- a/recipes/ucsc-positionaltblcheck/build.sh +++ b/recipes/ucsc-positionaltblcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/positionalTblCheck && make) -cp bin/positionalTblCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/positionalTblCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/positionalTblCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/positionalTblCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/positionalTblCheck" diff --git a/recipes/ucsc-positionaltblcheck/include.patch b/recipes/ucsc-positionaltblcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-positionaltblcheck/include.patch +++ b/recipes/ucsc-positionaltblcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-positionaltblcheck/meta.yaml b/recipes/ucsc-positionaltblcheck/meta.yaml index 022176abef7e4..1bd0671c85e27 100644 --- a/recipes/ucsc-positionaltblcheck/meta.yaml +++ b/recipes/ucsc-positionaltblcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-positionaltblcheck" %} {% set program = "positionalTblCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "check that positional tables are sorted" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslcat/build.sh b/recipes/ucsc-pslcat/build.sh index 8f0d19f7c40f9..ef4ae6bb97d3d 100644 --- a/recipes/ucsc-pslcat/build.sh +++ b/recipes/ucsc-pslcat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslCat && make) -cp bin/pslCat "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslCat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslCat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslCat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslCat" diff --git a/recipes/ucsc-pslcat/include.patch b/recipes/ucsc-pslcat/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslcat/include.patch +++ b/recipes/ucsc-pslcat/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslcat/meta.yaml b/recipes/ucsc-pslcat/meta.yaml index 21c04084ea807..84be38fe0d48b 100644 --- a/recipes/ucsc-pslcat/meta.yaml +++ b/recipes/ucsc-pslcat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcat" %} {% set program = "pslCat" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "concatenate psl files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslcdnafilter/build.sh b/recipes/ucsc-pslcdnafilter/build.sh index 05a21275d4c6d..6f9c17e7cba0b 100644 --- a/recipes/ucsc-pslcdnafilter/build.sh +++ b/recipes/ucsc-pslcdnafilter/build.sh @@ -1,14 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd kent/src/hg/pslCDnaFilter && make) -cp bin/pslCDnaFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslCDnaFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslCDnaFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslCDnaFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslCDnaFilter" diff --git a/recipes/ucsc-pslcdnafilter/include.patch b/recipes/ucsc-pslcdnafilter/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslcdnafilter/include.patch +++ b/recipes/ucsc-pslcdnafilter/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index 8807ae5634842..58d533a67e4ff 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcdnafilter" %} {% set program = "pslCDnaFilter" %} -{% set version = "445" %} -{% set sha256 = "c7abb5db6a5e16a79aefcee849d2b59dbc71ee112ca1e41fea0afb25229cf56c" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -14,39 +14,48 @@ source: - "include.patch" build: - skip: True # [osx] - number: 1 + skip: True # [osx] + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-pslcheck/build.sh b/recipes/ucsc-pslcheck/build.sh index 9b8ba14c30a7e..bea130066fb3d 100644 --- a/recipes/ucsc-pslcheck/build.sh +++ b/recipes/ucsc-pslcheck/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslCheck && make) -cp bin/pslCheck "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslCheck" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslCheck && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslCheck "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslCheck" diff --git a/recipes/ucsc-pslcheck/include.patch b/recipes/ucsc-pslcheck/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslcheck/include.patch +++ b/recipes/ucsc-pslcheck/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslcheck/meta.yaml b/recipes/ucsc-pslcheck/meta.yaml index bdb230d6bd710..58ac61563cab6 100644 --- a/recipes/ucsc-pslcheck/meta.yaml +++ b/recipes/ucsc-pslcheck/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslcheck" %} {% set program = "pslCheck" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,30 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "validate PSL files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + \ No newline at end of file diff --git a/recipes/ucsc-psldropoverlap/build.sh b/recipes/ucsc-psldropoverlap/build.sh index 3d6c3a2acdf28..8056852ba266e 100644 --- a/recipes/ucsc-psldropoverlap/build.sh +++ b/recipes/ucsc-psldropoverlap/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslDropOverlap && make) -cp bin/pslDropOverlap "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslDropOverlap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslDropOverlap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslDropOverlap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslDropOverlap" diff --git a/recipes/ucsc-psldropoverlap/include.patch b/recipes/ucsc-psldropoverlap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-psldropoverlap/include.patch +++ b/recipes/ucsc-psldropoverlap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-psldropoverlap/meta.yaml b/recipes/ucsc-psldropoverlap/meta.yaml index 69fc9e7fd456d..6e34ccd565410 100644 --- a/recipes/ucsc-psldropoverlap/meta.yaml +++ b/recipes/ucsc-psldropoverlap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psldropoverlap" %} {% set program = "pslDropOverlap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "deletes all overlapping self alignments. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslfilter/build.sh b/recipes/ucsc-pslfilter/build.sh index 45a8bda3a2219..cf8b855b41b42 100644 --- a/recipes/ucsc-pslfilter/build.sh +++ b/recipes/ucsc-pslfilter/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslFilter && make) -cp bin/pslFilter "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslFilter" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslFilter && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslFilter "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslFilter" diff --git a/recipes/ucsc-pslfilter/include.patch b/recipes/ucsc-pslfilter/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslfilter/include.patch +++ b/recipes/ucsc-pslfilter/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslfilter/meta.yaml b/recipes/ucsc-pslfilter/meta.yaml index 73d97517cbbee..3069b7da5417d 100644 --- a/recipes/ucsc-pslfilter/meta.yaml +++ b/recipes/ucsc-pslfilter/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslfilter" %} {% set program = "pslFilter" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "filter out psl file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslhisto/build.sh b/recipes/ucsc-pslhisto/build.sh index d1f0b2a1cdc0a..0e8b1fe8c5bf1 100644 --- a/recipes/ucsc-pslhisto/build.sh +++ b/recipes/ucsc-pslhisto/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslHisto && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslHisto "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslHisto" +cp bin/pslHisto "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslHisto" diff --git a/recipes/ucsc-pslhisto/meta.yaml b/recipes/ucsc-pslhisto/meta.yaml index 404d4c7f221a3..3f78d33a190b3 100644 --- a/recipes/ucsc-pslhisto/meta.yaml +++ b/recipes/ucsc-pslhisto/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslhisto" %} {% set program = "pslHisto" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,8 +43,8 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc. @@ -53,5 +53,8 @@ analyzed with R, textHistogram, etc. doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslliftsubrangeblat/build.sh b/recipes/ucsc-pslliftsubrangeblat/build.sh index 0e33ea9346038..a814a887df9b0 100644 --- a/recipes/ucsc-pslliftsubrangeblat/build.sh +++ b/recipes/ucsc-pslliftsubrangeblat/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/pslLiftSubrangeBlat && make) -cp bin/pslLiftSubrangeBlat "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslLiftSubrangeBlat" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/pslLiftSubrangeBlat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslLiftSubrangeBlat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslLiftSubrangeBlat" diff --git a/recipes/ucsc-pslliftsubrangeblat/include.patch b/recipes/ucsc-pslliftsubrangeblat/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslliftsubrangeblat/include.patch +++ b/recipes/ucsc-pslliftsubrangeblat/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslliftsubrangeblat/meta.yaml b/recipes/ucsc-pslliftsubrangeblat/meta.yaml index fecad941cbb28..2265313198cd4 100644 --- a/recipes/ucsc-pslliftsubrangeblat/meta.yaml +++ b/recipes/ucsc-pslliftsubrangeblat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslliftsubrangeblat" %} {% set program = "pslLiftSubrangeBlat" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "lift PSLs from blat subrange alignments" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslmap/build.sh b/recipes/ucsc-pslmap/build.sh index a50ee2333c360..dc5c2fd9f25d7 100644 --- a/recipes/ucsc-pslmap/build.sh +++ b/recipes/ucsc-pslmap/build.sh @@ -1,14 +1,22 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/stringify && make) -(cd kent/src/hg/utils/pslMap && make) -cp bin/pslMap "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslMap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslMap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslMap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslMap" diff --git a/recipes/ucsc-pslmap/include.patch b/recipes/ucsc-pslmap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslmap/include.patch +++ b/recipes/ucsc-pslmap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslmap/meta.yaml b/recipes/ucsc-pslmap/meta.yaml index 2c144a480b637..df0c23ae1a8c3 100644 --- a/recipes/ucsc-pslmap/meta.yaml +++ b/recipes/ucsc-pslmap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslmap" %} {% set program = "pslMap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 1 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "map PSLs alignments to new targets using alignments of" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslmappostchain/build.sh b/recipes/ucsc-pslmappostchain/build.sh index 54453ecba698c..5eadb4481a518 100644 --- a/recipes/ucsc-pslmappostchain/build.sh +++ b/recipes/ucsc-pslmappostchain/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/pslMapPostChain && make) -cp bin/pslMapPostChain "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslMapPostChain" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslMapPostChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslMapPostChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslMapPostChain" diff --git a/recipes/ucsc-pslmappostchain/include.patch b/recipes/ucsc-pslmappostchain/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslmappostchain/include.patch +++ b/recipes/ucsc-pslmappostchain/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslmappostchain/meta.yaml b/recipes/ucsc-pslmappostchain/meta.yaml index b2906a3216d1f..7c51187e06db4 100644 --- a/recipes/ucsc-pslmappostchain/meta.yaml +++ b/recipes/ucsc-pslmappostchain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslmappostchain" %} {% set program = "pslMapPostChain" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,27 +27,36 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues. " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslmrnacover/build.sh b/recipes/ucsc-pslmrnacover/build.sh index a7c9804cb5f4a..9cff5cb571c0e 100644 --- a/recipes/ucsc-pslmrnacover/build.sh +++ b/recipes/ucsc-pslmrnacover/build.sh @@ -17,5 +17,5 @@ mkdir -p "${BINDIR}" (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/mouseStuff/pslMrnaCover && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslMrnaCover "${PREFIX}/bin" +cp bin/pslMrnaCover "${PREFIX}/bin" chmod 0755 "${PREFIX}/bin/pslMrnaCover" diff --git a/recipes/ucsc-pslmrnacover/meta.yaml b/recipes/ucsc-pslmrnacover/meta.yaml index 3b0628781bcd1..a50e026a5250b 100644 --- a/recipes/ucsc-pslmrnacover/meta.yaml +++ b/recipes/ucsc-pslmrnacover/meta.yaml @@ -50,5 +50,8 @@ about: doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslpairs/build.sh b/recipes/ucsc-pslpairs/build.sh index a90d13ee108cb..6cd14191ba17c 100644 --- a/recipes/ucsc-pslpairs/build.sh +++ b/recipes/ucsc-pslpairs/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -(cd kent/src/hg/lib && USE_HIC=0 make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslPairs && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslPairs "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslPairs" +cp bin/pslPairs "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPairs" diff --git a/recipes/ucsc-pslpairs/meta.yaml b/recipes/ucsc-pslpairs/meta.yaml index b581d5d417072..73161b3ec6fb7 100644 --- a/recipes/ucsc-pslpairs/meta.yaml +++ b/recipes/ucsc-pslpairs/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpairs" %} {% set program = "pslPairs" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "join paired ends in psl alignments" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslpartition/build.sh b/recipes/ucsc-pslpartition/build.sh index 3a4209e4f50cf..291e7d801ec0b 100644 --- a/recipes/ucsc-pslpartition/build.sh +++ b/recipes/ucsc-pslpartition/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslPartition && make) -cp bin/pslPartition "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslPartition" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslPartition && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslPartition "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPartition" diff --git a/recipes/ucsc-pslpartition/include.patch b/recipes/ucsc-pslpartition/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslpartition/include.patch +++ b/recipes/ucsc-pslpartition/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslpartition/meta.yaml b/recipes/ucsc-pslpartition/meta.yaml index 11df1060d2279..377e85b51ecf5 100644 --- a/recipes/ucsc-pslpartition/meta.yaml +++ b/recipes/ucsc-pslpartition/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpartition" %} {% set program = "pslPartition" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "split PSL files into non-overlapping sets" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslpostarget/build.sh b/recipes/ucsc-pslpostarget/build.sh index a69900e05adbd..fb27dca9ad942 100644 --- a/recipes/ucsc-pslpostarget/build.sh +++ b/recipes/ucsc-pslpostarget/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/pslPosTarget && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslPosTarget "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslPosTarget" +cp bin/pslPosTarget "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPosTarget" diff --git a/recipes/ucsc-pslpostarget/meta.yaml b/recipes/ucsc-pslpostarget/meta.yaml index 7dfaf50fd3ce5..8172abd6a6979 100644 --- a/recipes/ucsc-pslpostarget/meta.yaml +++ b/recipes/ucsc-pslpostarget/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpostarget" %} {% set program = "pslPosTarget" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "flip psl strands so target is positive and implicit" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslpretty/build.sh b/recipes/ucsc-pslpretty/build.sh index 89c3ce9725e23..f4d1451c7c558 100644 --- a/recipes/ucsc-pslpretty/build.sh +++ b/recipes/ucsc-pslpretty/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslPretty && make) -cp bin/pslPretty "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslPretty" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslPretty && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslPretty "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslPretty" diff --git a/recipes/ucsc-pslpretty/include.patch b/recipes/ucsc-pslpretty/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslpretty/include.patch +++ b/recipes/ucsc-pslpretty/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslpretty/meta.yaml b/recipes/ucsc-pslpretty/meta.yaml index 9810dafca6c09..e2db3fedad559 100644 --- a/recipes/ucsc-pslpretty/meta.yaml +++ b/recipes/ucsc-pslpretty/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslpretty" %} {% set program = "pslPretty" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert PSL to human-readable output" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslrc/build.sh b/recipes/ucsc-pslrc/build.sh index 03b0eed50d4cd..6ca282e519ca1 100644 --- a/recipes/ucsc-pslrc/build.sh +++ b/recipes/ucsc-pslrc/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/pslRc && make) -cp bin/pslRc "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslRc" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslRc && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslRc "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslRc" diff --git a/recipes/ucsc-pslrc/include.patch b/recipes/ucsc-pslrc/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslrc/include.patch +++ b/recipes/ucsc-pslrc/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslrc/meta.yaml b/recipes/ucsc-pslrc/meta.yaml index a42ca7ee23c4d..3ac6f82f47dfe 100644 --- a/recipes/ucsc-pslrc/meta.yaml +++ b/recipes/ucsc-pslrc/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslrc" %} {% set program = "pslRc" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "reverse-complement psl" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslrecalcmatch/build.sh b/recipes/ucsc-pslrecalcmatch/build.sh index 41a0a5d53edfe..17f174080a9f0 100644 --- a/recipes/ucsc-pslrecalcmatch/build.sh +++ b/recipes/ucsc-pslrecalcmatch/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslRecalcMatch && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslRecalcMatch "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslRecalcMatch" +cp bin/pslRecalcMatch "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslRecalcMatch" diff --git a/recipes/ucsc-pslrecalcmatch/meta.yaml b/recipes/ucsc-pslrecalcmatch/meta.yaml index ecff808f4ac50..3a6b62e0f316b 100644 --- a/recipes/ucsc-pslrecalcmatch/meta.yaml +++ b/recipes/ucsc-pslrecalcmatch/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslrecalcmatch" %} {% set program = "pslRecalcMatch" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Recalculate match,mismatch,repMatch columns in psl file." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslreps/build.sh b/recipes/ucsc-pslreps/build.sh index adbe151df2566..fa9e34309baed 100644 --- a/recipes/ucsc-pslreps/build.sh +++ b/recipes/ucsc-pslreps/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslReps && make) -cp bin/pslReps "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslReps" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslReps && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslReps "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslReps" diff --git a/recipes/ucsc-pslreps/include.patch b/recipes/ucsc-pslreps/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslreps/include.patch +++ b/recipes/ucsc-pslreps/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslreps/meta.yaml b/recipes/ucsc-pslreps/meta.yaml index 450be1b4a1e2c..a6430c181ea3c 100644 --- a/recipes/ucsc-pslreps/meta.yaml +++ b/recipes/ucsc-pslreps/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslreps" %} {% set program = "pslReps" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Analyze repeats and generate genome-wide best alignments from a" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslscore/build.sh b/recipes/ucsc-pslscore/build.sh index 1a0fa041d5306..874a7d983f790 100644 --- a/recipes/ucsc-pslscore/build.sh +++ b/recipes/ucsc-pslscore/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/pslScore && make) -cp bin/pslScore "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslScore" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslScore && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslScore "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslScore" diff --git a/recipes/ucsc-pslscore/include.patch b/recipes/ucsc-pslscore/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslscore/include.patch +++ b/recipes/ucsc-pslscore/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslscore/meta.yaml b/recipes/ucsc-pslscore/meta.yaml index 5be496a84abbb..1476a30e87a17 100644 --- a/recipes/ucsc-pslscore/meta.yaml +++ b/recipes/ucsc-pslscore/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslscore" %} {% set program = "pslScore" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "calculate web blat score from psl files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslselect/build.sh b/recipes/ucsc-pslselect/build.sh index 661a81177c6c2..c9df1304a0391 100644 --- a/recipes/ucsc-pslselect/build.sh +++ b/recipes/ucsc-pslselect/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslSelect && make) -cp bin/pslSelect "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslSelect" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslSelect && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslSelect "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSelect" diff --git a/recipes/ucsc-pslselect/include.patch b/recipes/ucsc-pslselect/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslselect/include.patch +++ b/recipes/ucsc-pslselect/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslselect/meta.yaml b/recipes/ucsc-pslselect/meta.yaml index 94e42706a0ac7..58d456a600295 100644 --- a/recipes/ucsc-pslselect/meta.yaml +++ b/recipes/ucsc-pslselect/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslselect" %} {% set program = "pslSelect" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "select records from a PSL file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslsomerecords/build.sh b/recipes/ucsc-pslsomerecords/build.sh index c7390660855d1..ad88b60584d55 100644 --- a/recipes/ucsc-pslsomerecords/build.sh +++ b/recipes/ucsc-pslsomerecords/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslSomeRecords && make) -cp bin/pslSomeRecords "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslSomeRecords" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslSomeRecords && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslSomeRecords "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSomeRecords" diff --git a/recipes/ucsc-pslsomerecords/include.patch b/recipes/ucsc-pslsomerecords/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslsomerecords/include.patch +++ b/recipes/ucsc-pslsomerecords/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslsomerecords/meta.yaml b/recipes/ucsc-pslsomerecords/meta.yaml index 1bc820c6a1f16..5af9a55a1dad2 100644 --- a/recipes/ucsc-pslsomerecords/meta.yaml +++ b/recipes/ucsc-pslsomerecords/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslsomerecords" %} {% set program = "pslSomeRecords" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Extract multiple psl records" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslsort/build.sh b/recipes/ucsc-pslsort/build.sh index b18c33998499e..046c3d78cb35f 100644 --- a/recipes/ucsc-pslsort/build.sh +++ b/recipes/ucsc-pslsort/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslSort && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslSort "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslSort" +cp bin/pslSort "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSort" diff --git a/recipes/ucsc-pslsort/meta.yaml b/recipes/ucsc-pslsort/meta.yaml index 79c34e14b5ec6..5e7ae26baeb3f 100644 --- a/recipes/ucsc-pslsort/meta.yaml +++ b/recipes/ucsc-pslsort/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslsort" %} {% set program = "pslSort" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Merge and sort psCluster .psl output files" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-pslstats/build.sh b/recipes/ucsc-pslstats/build.sh index e010d560bb0c1..5955bcc8bc430 100644 --- a/recipes/ucsc-pslstats/build.sh +++ b/recipes/ucsc-pslstats/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslStats && make) -cp bin/pslStats "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslStats" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslStats && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslStats "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslStats" diff --git a/recipes/ucsc-pslstats/include.patch b/recipes/ucsc-pslstats/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslstats/include.patch +++ b/recipes/ucsc-pslstats/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslstats/meta.yaml b/recipes/ucsc-pslstats/meta.yaml index 9a3e3b0f48491..df4dcdf568dde 100644 --- a/recipes/ucsc-pslstats/meta.yaml +++ b/recipes/ucsc-pslstats/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslstats" %} {% set program = "pslStats" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "collect statistics from a psl file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslswap/build.sh b/recipes/ucsc-pslswap/build.sh index 0b4455e51c576..e1bbe56df4c19 100644 --- a/recipes/ucsc-pslswap/build.sh +++ b/recipes/ucsc-pslswap/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslSwap && make) -cp bin/pslSwap "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslSwap" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslSwap && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslSwap "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslSwap" diff --git a/recipes/ucsc-pslswap/include.patch b/recipes/ucsc-pslswap/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslswap/include.patch +++ b/recipes/ucsc-pslswap/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslswap/meta.yaml b/recipes/ucsc-pslswap/meta.yaml index 3d086d16daa16..034f5d8fb55c0 100644 --- a/recipes/ucsc-pslswap/meta.yaml +++ b/recipes/ucsc-pslswap/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslswap" %} {% set program = "pslSwap" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,24 +27,33 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " Swap target and query in psls " + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-psltobed/build.sh b/recipes/ucsc-psltobed/build.sh index aad6779233d63..7280bbec84dfc 100644 --- a/recipes/ucsc-psltobed/build.sh +++ b/recipes/ucsc-psltobed/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslToBed && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslToBed "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslToBed" +cp bin/pslToBed "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToBed" diff --git a/recipes/ucsc-psltobed/meta.yaml b/recipes/ucsc-psltobed/meta.yaml index b80b18d71a5c4..470ba825d07d8 100644 --- a/recipes/ucsc-psltobed/meta.yaml +++ b/recipes/ucsc-psltobed/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltobed" %} {% set program = "pslToBed" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,8 +43,8 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: " transform a psl format file to a bed format file. " @@ -52,5 +52,8 @@ transform a psl format file to a bed format file. doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-psltobigpsl/build.sh b/recipes/ucsc-psltobigpsl/build.sh index 3e1f3486afb2c..905ffabb5bda3 100644 --- a/recipes/ucsc-psltobigpsl/build.sh +++ b/recipes/ucsc-psltobigpsl/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/pslToBigPsl && make) -cp bin/pslToBigPsl "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslToBigPsl" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/pslToBigPsl && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslToBigPsl "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToBigPsl" diff --git a/recipes/ucsc-psltobigpsl/include.patch b/recipes/ucsc-psltobigpsl/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-psltobigpsl/include.patch +++ b/recipes/ucsc-psltobigpsl/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-psltobigpsl/meta.yaml b/recipes/ucsc-psltobigpsl/meta.yaml index 2682f3653cd23..025a1c65a4b10 100644 --- a/recipes/ucsc-psltobigpsl/meta.yaml +++ b/recipes/ucsc-psltobigpsl/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltobigpsl" %} {% set program = "pslToBigPsl" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 5 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "converts psl to bigPsl input (bed format with extra fields)" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-psltochain/build.sh b/recipes/ucsc-psltochain/build.sh index 4d4568b0f1411..ef1f2a4b3cbc2 100644 --- a/recipes/ucsc-psltochain/build.sh +++ b/recipes/ucsc-psltochain/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/pslToChain && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/pslToChain "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/pslToChain" +cp bin/pslToChain "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToChain" diff --git a/recipes/ucsc-psltochain/meta.yaml b/recipes/ucsc-psltochain/meta.yaml index c851e92f46935..87146c0c41407 100644 --- a/recipes/ucsc-psltochain/meta.yaml +++ b/recipes/ucsc-psltochain/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltochain" %} {% set program = "pslToChain" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert psl records to chain records " dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-psltopslx/build.sh b/recipes/ucsc-psltopslx/build.sh index 5dbb6b7a422ec..922799ae7f212 100644 --- a/recipes/ucsc-psltopslx/build.sh +++ b/recipes/ucsc-psltopslx/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/pslToPslx && make) -cp bin/pslToPslx "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslToPslx" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/pslToPslx && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslToPslx "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslToPslx" diff --git a/recipes/ucsc-psltopslx/include.patch b/recipes/ucsc-psltopslx/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-psltopslx/include.patch +++ b/recipes/ucsc-psltopslx/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-psltopslx/meta.yaml b/recipes/ucsc-psltopslx/meta.yaml index 77454025bf7f0..cefae969c7fcd 100644 --- a/recipes/ucsc-psltopslx/meta.yaml +++ b/recipes/ucsc-psltopslx/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-psltopslx" %} {% set program = "pslToPslx" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert from psl to pslx format, which includes sequences" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-pslxtofa/build.sh b/recipes/ucsc-pslxtofa/build.sh index 863aec4ce315e..1f69a506672c3 100644 --- a/recipes/ucsc-pslxtofa/build.sh +++ b/recipes/ucsc-pslxtofa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/pslxToFa && make) -cp bin/pslxToFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/pslxToFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/pslxToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/pslxToFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/pslxToFa" diff --git a/recipes/ucsc-pslxtofa/include.patch b/recipes/ucsc-pslxtofa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-pslxtofa/include.patch +++ b/recipes/ucsc-pslxtofa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-pslxtofa/meta.yaml b/recipes/ucsc-pslxtofa/meta.yaml index 67df737ea1129..25bb9bac1eb2d 100644 --- a/recipes/ucsc-pslxtofa/meta.yaml +++ b/recipes/ucsc-pslxtofa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-pslxtofa" %} {% set program = "pslxToFa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert pslx (with sequence) to fasta file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qacagplift/build.sh b/recipes/ucsc-qacagplift/build.sh index 1bc5422348f6d..c964a8d70f369 100644 --- a/recipes/ucsc-qacagplift/build.sh +++ b/recipes/ucsc-qacagplift/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qacAgpLift && make) -cp bin/qacAgpLift "$PREFIX/bin" -chmod +x "$PREFIX/bin/qacAgpLift" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qacAgpLift && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qacAgpLift "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qacAgpLift" diff --git a/recipes/ucsc-qacagplift/include.patch b/recipes/ucsc-qacagplift/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qacagplift/include.patch +++ b/recipes/ucsc-qacagplift/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qacagplift/meta.yaml b/recipes/ucsc-qacagplift/meta.yaml index eac8a25f5ecf4..d801311aa1b38 100644 --- a/recipes/ucsc-qacagplift/meta.yaml +++ b/recipes/ucsc-qacagplift/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qacagplift" %} {% set program = "qacAgpLift" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Use AGP to combine per-scaffold qac into per-chrom qac." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qactoqa/build.sh b/recipes/ucsc-qactoqa/build.sh index e48a8804dd3e7..9eaa54e5d80b4 100644 --- a/recipes/ucsc-qactoqa/build.sh +++ b/recipes/ucsc-qactoqa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qacToQa && make) -cp bin/qacToQa "$PREFIX/bin" -chmod +x "$PREFIX/bin/qacToQa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qacToQa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qacToQa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qacToQa" diff --git a/recipes/ucsc-qactoqa/include.patch b/recipes/ucsc-qactoqa/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qactoqa/include.patch +++ b/recipes/ucsc-qactoqa/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qactoqa/meta.yaml b/recipes/ucsc-qactoqa/meta.yaml index 0fbf3dbd9b67e..510d12750220f 100644 --- a/recipes/ucsc-qactoqa/meta.yaml +++ b/recipes/ucsc-qactoqa/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qactoqa" %} {% set program = "qacToQa" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert from compressed to uncompressed" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-qactowig/build.sh b/recipes/ucsc-qactowig/build.sh index 2cfa1d2934098..d39a37b27c18b 100644 --- a/recipes/ucsc-qactowig/build.sh +++ b/recipes/ucsc-qactowig/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/qacToWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/qacToWig "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/qacToWig" +cp bin/qacToWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qacToWig" diff --git a/recipes/ucsc-qactowig/meta.yaml b/recipes/ucsc-qactowig/meta.yaml index 0b905003df6a4..86bbbe0154949 100644 --- a/recipes/ucsc-qactowig/meta.yaml +++ b/recipes/ucsc-qactowig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qactowig" %} {% set program = "qacToWig" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert from compressed quality score format to wiggle format." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-qatoqac/build.sh b/recipes/ucsc-qatoqac/build.sh index 0211aa66be612..413392663e72b 100644 --- a/recipes/ucsc-qatoqac/build.sh +++ b/recipes/ucsc-qatoqac/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/qaToQac && make) -cp bin/qaToQac "$PREFIX/bin" -chmod +x "$PREFIX/bin/qaToQac" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/qaToQac && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/qaToQac "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/qaToQac" diff --git a/recipes/ucsc-qatoqac/include.patch b/recipes/ucsc-qatoqac/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-qatoqac/include.patch +++ b/recipes/ucsc-qatoqac/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-qatoqac/meta.yaml b/recipes/ucsc-qatoqac/meta.yaml index 5b77b89af8a07..2cdd1b678e576 100644 --- a/recipes/ucsc-qatoqac/meta.yaml +++ b/recipes/ucsc-qatoqac/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-qatoqac" %} {% set program = "qaToQac" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert from uncompressed to compressed" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-randomlines/build.sh b/recipes/ucsc-randomlines/build.sh index e180d45f77b14..ea6b63b0d2966 100644 --- a/recipes/ucsc-randomlines/build.sh +++ b/recipes/ucsc-randomlines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/randomLines && make) -cp bin/randomLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/randomLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/randomLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/randomLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/randomLines" diff --git a/recipes/ucsc-randomlines/include.patch b/recipes/ucsc-randomlines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-randomlines/include.patch +++ b/recipes/ucsc-randomlines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-randomlines/meta.yaml b/recipes/ucsc-randomlines/meta.yaml index b3923f83b759d..b186f57343ca7 100644 --- a/recipes/ucsc-randomlines/meta.yaml +++ b/recipes/ucsc-randomlines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-randomlines" %} {% set program = "randomLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Pick out random lines from file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-rasqlquery/build.sh b/recipes/ucsc-rasqlquery/build.sh index 8973924b1eb3e..82a20c81779f9 100644 --- a/recipes/ucsc-rasqlquery/build.sh +++ b/recipes/ucsc-rasqlquery/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raSqlQuery && make) -cp bin/raSqlQuery "$PREFIX/bin" -chmod +x "$PREFIX/bin/raSqlQuery" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/raSqlQuery && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/raSqlQuery "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/raSqlQuery" diff --git a/recipes/ucsc-rasqlquery/include.patch b/recipes/ucsc-rasqlquery/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-rasqlquery/include.patch +++ b/recipes/ucsc-rasqlquery/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-rasqlquery/meta.yaml b/recipes/ucsc-rasqlquery/meta.yaml index b61951542b664..e4044def021c6 100644 --- a/recipes/ucsc-rasqlquery/meta.yaml +++ b/recipes/ucsc-rasqlquery/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-rasqlquery" %} {% set program = "raSqlQuery" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Do a SQL-like query on a RA file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ratolines/build.sh b/recipes/ucsc-ratolines/build.sh index f7bda7baaa8f9..aee4cda65ffba 100644 --- a/recipes/ucsc-ratolines/build.sh +++ b/recipes/ucsc-ratolines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raToLines && make) -cp bin/raToLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/raToLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/raToLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/raToLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/raToLines" diff --git a/recipes/ucsc-ratolines/include.patch b/recipes/ucsc-ratolines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ratolines/include.patch +++ b/recipes/ucsc-ratolines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ratolines/meta.yaml b/recipes/ucsc-ratolines/meta.yaml index b7e5b58948156..2b95786fa9a09 100644 --- a/recipes/ucsc-ratolines/meta.yaml +++ b/recipes/ucsc-ratolines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ratolines" %} {% set program = "raToLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Output .ra file stanzas as single lines, with pipe-separated fields." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ratotab/build.sh b/recipes/ucsc-ratotab/build.sh index 376e0b2cb6681..6ef3bb6dbe25c 100644 --- a/recipes/ucsc-ratotab/build.sh +++ b/recipes/ucsc-ratotab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/raToTab && make) -cp bin/raToTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/raToTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/raToTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/raToTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/raToTab" diff --git a/recipes/ucsc-ratotab/include.patch b/recipes/ucsc-ratotab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ratotab/include.patch +++ b/recipes/ucsc-ratotab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ratotab/meta.yaml b/recipes/ucsc-ratotab/meta.yaml index 2e41461139f83..a0318e0be1bf6 100644 --- a/recipes/ucsc-ratotab/meta.yaml +++ b/recipes/ucsc-ratotab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ratotab" %} {% set program = "raToTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert ra file to table." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-rmfadups/build.sh b/recipes/ucsc-rmfadups/build.sh index b7cedf268cbd0..74f2d3bec2e33 100644 --- a/recipes/ucsc-rmfadups/build.sh +++ b/recipes/ucsc-rmfadups/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/rmFaDups && make) -cp bin/rmFaDups "$PREFIX/bin" -chmod +x "$PREFIX/bin/rmFaDups" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/rmFaDups && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/rmFaDups "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/rmFaDups" diff --git a/recipes/ucsc-rmfadups/include.patch b/recipes/ucsc-rmfadups/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-rmfadups/include.patch +++ b/recipes/ucsc-rmfadups/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-rmfadups/meta.yaml b/recipes/ucsc-rmfadups/meta.yaml index 6c578746a3630..3219c579197fb 100644 --- a/recipes/ucsc-rmfadups/meta.yaml +++ b/recipes/ucsc-rmfadups/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-rmfadups" %} {% set program = "rmFaDups" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "remove duplicate records in FA file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-rowstocols/build.sh b/recipes/ucsc-rowstocols/build.sh index f4c4bb2ade3fd..233ebf5926753 100644 --- a/recipes/ucsc-rowstocols/build.sh +++ b/recipes/ucsc-rowstocols/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/rowsToCols && make) -cp bin/rowsToCols "$PREFIX/bin" -chmod +x "$PREFIX/bin/rowsToCols" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/rowsToCols && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/rowsToCols "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/rowsToCols" diff --git a/recipes/ucsc-rowstocols/include.patch b/recipes/ucsc-rowstocols/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-rowstocols/include.patch +++ b/recipes/ucsc-rowstocols/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-rowstocols/meta.yaml b/recipes/ucsc-rowstocols/meta.yaml index 5996bb1425ee0..3b9bf1fc1db8b 100644 --- a/recipes/ucsc-rowstocols/meta.yaml +++ b/recipes/ucsc-rowstocols/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-rowstocols" %} {% set program = "rowsToCols" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert rows to columns and vice versa in a text file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-spacedtotab/build.sh b/recipes/ucsc-spacedtotab/build.sh index 6327bb4f36c3e..1a1c572360a7e 100644 --- a/recipes/ucsc-spacedtotab/build.sh +++ b/recipes/ucsc-spacedtotab/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/spacedToTab && make) -cp bin/spacedToTab "$PREFIX/bin" -chmod +x "$PREFIX/bin/spacedToTab" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/spacedToTab && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/spacedToTab "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/spacedToTab" diff --git a/recipes/ucsc-spacedtotab/include.patch b/recipes/ucsc-spacedtotab/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-spacedtotab/include.patch +++ b/recipes/ucsc-spacedtotab/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-spacedtotab/meta.yaml b/recipes/ucsc-spacedtotab/meta.yaml index d14f6086ea2dc..1f7c293aafb21 100644 --- a/recipes/ucsc-spacedtotab/meta.yaml +++ b/recipes/ucsc-spacedtotab/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-spacedtotab" %} {% set program = "spacedToTab" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert fixed width space separated fields to tab separated" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-splitfile/build.sh b/recipes/ucsc-splitfile/build.sh index e4cbfae5d5da6..0b085f08fe8bd 100644 --- a/recipes/ucsc-splitfile/build.sh +++ b/recipes/ucsc-splitfile/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/splitFile && make) -cp bin/splitFile "$PREFIX/bin" -chmod +x "$PREFIX/bin/splitFile" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/splitFile && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/splitFile "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/splitFile" diff --git a/recipes/ucsc-splitfile/include.patch b/recipes/ucsc-splitfile/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-splitfile/include.patch +++ b/recipes/ucsc-splitfile/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-splitfile/meta.yaml b/recipes/ucsc-splitfile/meta.yaml index d7462e408fdb9..e893afcb87139 100644 --- a/recipes/ucsc-splitfile/meta.yaml +++ b/recipes/ucsc-splitfile/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-splitfile" %} {% set program = "splitFile" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split up a file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-splitfilebycolumn/build.sh b/recipes/ucsc-splitfilebycolumn/build.sh index b15b6afb70873..7b1ed691f5fc8 100644 --- a/recipes/ucsc-splitfilebycolumn/build.sh +++ b/recipes/ucsc-splitfilebycolumn/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/splitFileByColumn && make) -cp bin/splitFileByColumn "$PREFIX/bin" -chmod +x "$PREFIX/bin/splitFileByColumn" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/splitFileByColumn && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/splitFileByColumn "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/splitFileByColumn" diff --git a/recipes/ucsc-splitfilebycolumn/include.patch b/recipes/ucsc-splitfilebycolumn/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-splitfilebycolumn/include.patch +++ b/recipes/ucsc-splitfilebycolumn/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-splitfilebycolumn/meta.yaml b/recipes/ucsc-splitfilebycolumn/meta.yaml index aebb3eae685cb..4bab401fc02c4 100644 --- a/recipes/ucsc-splitfilebycolumn/meta.yaml +++ b/recipes/ucsc-splitfilebycolumn/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-splitfilebycolumn" %} {% set program = "splitFileByColumn" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Split text input into files named by column value" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-sqltoxml/build.sh b/recipes/ucsc-sqltoxml/build.sh index 825908cd3ff6b..2e84672942070 100644 --- a/recipes/ucsc-sqltoxml/build.sh +++ b/recipes/ucsc-sqltoxml/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/sqlToXml && make) -cp bin/sqlToXml "$PREFIX/bin" -chmod +x "$PREFIX/bin/sqlToXml" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/sqlToXml && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/sqlToXml "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/sqlToXml" diff --git a/recipes/ucsc-sqltoxml/include.patch b/recipes/ucsc-sqltoxml/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-sqltoxml/include.patch +++ b/recipes/ucsc-sqltoxml/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-sqltoxml/meta.yaml b/recipes/ucsc-sqltoxml/meta.yaml index 3556ed5c11082..690ca5a345e3b 100644 --- a/recipes/ucsc-sqltoxml/meta.yaml +++ b/recipes/ucsc-sqltoxml/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-sqltoxml" %} {% set program = "sqlToXml" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "dump out all or part of a relational database to XML, guided" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-stringify/build.sh b/recipes/ucsc-stringify/build.sh index 8a122223b89ca..431d016c0f80d 100644 --- a/recipes/ucsc-stringify/build.sh +++ b/recipes/ucsc-stringify/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/stringify && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/stringify "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/stringify" +cp bin/stringify "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/stringify" diff --git a/recipes/ucsc-stringify/meta.yaml b/recipes/ucsc-stringify/meta.yaml index b11c925f68302..32b2c0585670b 100644 --- a/recipes/ucsc-stringify/meta.yaml +++ b/recipes/ucsc-stringify/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-stringify" %} {% set program = "stringify" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -17,7 +17,7 @@ build: skip: True # [osx] number: 0 run_exports: - - {{ pin_subpackage(package, max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert file to C strings" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-subchar/build.sh b/recipes/ucsc-subchar/build.sh index 5129d2652ab3b..0e64313706326 100644 --- a/recipes/ucsc-subchar/build.sh +++ b/recipes/ucsc-subchar/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/subChar && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/subChar "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/subChar" +cp bin/subChar "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/subChar" diff --git a/recipes/ucsc-subchar/meta.yaml b/recipes/ucsc-subchar/meta.yaml index 10b943776e59c..58f2a5ab8d6c0 100644 --- a/recipes/ucsc-subchar/meta.yaml +++ b/recipes/ucsc-subchar/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-subchar" %} {% set program = "subChar" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Substitute one character for another throughout a file." dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-subcolumn/build.sh b/recipes/ucsc-subcolumn/build.sh index 3373060867eb0..4e7e3c1492639 100644 --- a/recipes/ucsc-subcolumn/build.sh +++ b/recipes/ucsc-subcolumn/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/subColumn && make) -cp bin/subColumn "$PREFIX/bin" -chmod +x "$PREFIX/bin/subColumn" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/subColumn && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/subColumn "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/subColumn" diff --git a/recipes/ucsc-subcolumn/include.patch b/recipes/ucsc-subcolumn/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-subcolumn/include.patch +++ b/recipes/ucsc-subcolumn/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-subcolumn/meta.yaml b/recipes/ucsc-subcolumn/meta.yaml index 8a5c7293c3be4..f481ad2ca4aba 100644 --- a/recipes/ucsc-subcolumn/meta.yaml +++ b/recipes/ucsc-subcolumn/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-subcolumn" %} {% set program = "subColumn" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Substitute one column in a tab-separated file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-taillines/build.sh b/recipes/ucsc-taillines/build.sh index 1d3d8478855c2..31b3b4954aa6c 100644 --- a/recipes/ucsc-taillines/build.sh +++ b/recipes/ucsc-taillines/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/tailLines && make) -cp bin/tailLines "$PREFIX/bin" -chmod +x "$PREFIX/bin/tailLines" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/tailLines && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/tailLines "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/tailLines" diff --git a/recipes/ucsc-taillines/include.patch b/recipes/ucsc-taillines/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-taillines/include.patch +++ b/recipes/ucsc-taillines/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-taillines/meta.yaml b/recipes/ucsc-taillines/meta.yaml index 610642e21c3f4..5b2df04b6411d 100644 --- a/recipes/ucsc-taillines/meta.yaml +++ b/recipes/ucsc-taillines/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-taillines" %} {% set program = "tailLines" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "add tail to each line of file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-tdbquery/build.sh b/recipes/ucsc-tdbquery/build.sh index 2a385dd48fddb..0111e2ceb8681 100644 --- a/recipes/ucsc-tdbquery/build.sh +++ b/recipes/ucsc-tdbquery/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/tdbQuery && make) -cp bin/tdbQuery "$PREFIX/bin" -chmod +x "$PREFIX/bin/tdbQuery" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/tdbQuery && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/tdbQuery "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/tdbQuery" diff --git a/recipes/ucsc-tdbquery/include.patch b/recipes/ucsc-tdbquery/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-tdbquery/include.patch +++ b/recipes/ucsc-tdbquery/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-tdbquery/meta.yaml b/recipes/ucsc-tdbquery/meta.yaml index 3d46b7ee704a2..435e3e83544bf 100644 --- a/recipes/ucsc-tdbquery/meta.yaml +++ b/recipes/ucsc-tdbquery/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-tdbquery" %} {% set program = "tdbQuery" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Query the trackDb system using SQL syntax." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-texthistogram/build.sh b/recipes/ucsc-texthistogram/build.sh index 0b14714882311..4b83a0c70f4e6 100644 --- a/recipes/ucsc-texthistogram/build.sh +++ b/recipes/ucsc-texthistogram/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/textHistogram && make) -cp bin/textHistogram "$PREFIX/bin" -chmod +x "$PREFIX/bin/textHistogram" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/textHistogram && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/textHistogram "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/textHistogram" diff --git a/recipes/ucsc-texthistogram/include.patch b/recipes/ucsc-texthistogram/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-texthistogram/include.patch +++ b/recipes/ucsc-texthistogram/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-texthistogram/meta.yaml b/recipes/ucsc-texthistogram/meta.yaml index 087acaeef8301..756b419e8949d 100644 --- a/recipes/ucsc-texthistogram/meta.yaml +++ b/recipes/ucsc-texthistogram/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-texthistogram" %} {% set program = "textHistogram" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Make a histogram in ascii" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-ticktodate/build.sh b/recipes/ucsc-ticktodate/build.sh index 1fb966c199fe3..576694c3ec6fe 100644 --- a/recipes/ucsc-ticktodate/build.sh +++ b/recipes/ucsc-ticktodate/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/tickToDate && make) -cp bin/tickToDate "$PREFIX/bin" -chmod +x "$PREFIX/bin/tickToDate" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/tickToDate && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/tickToDate "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/tickToDate" diff --git a/recipes/ucsc-ticktodate/include.patch b/recipes/ucsc-ticktodate/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-ticktodate/include.patch +++ b/recipes/ucsc-ticktodate/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-ticktodate/meta.yaml b/recipes/ucsc-ticktodate/meta.yaml index 0e2ca23327479..ac0059144d920 100644 --- a/recipes/ucsc-ticktodate/meta.yaml +++ b/recipes/ucsc-ticktodate/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-ticktodate" %} {% set program = "tickToDate" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert seconds since 1970 to time and date" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-tolower/build.sh b/recipes/ucsc-tolower/build.sh index c59cd1a12634d..1208c312db8dd 100644 --- a/recipes/ucsc-tolower/build.sh +++ b/recipes/ucsc-tolower/build.sh @@ -2,20 +2,20 @@ set -xe -mkdir -p "$PREFIX/bin" +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/utils/toLower && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/toLower "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/toLower" +cp bin/toLower "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/toLower" diff --git a/recipes/ucsc-tolower/meta.yaml b/recipes/ucsc-tolower/meta.yaml index 076b34215d2e8..332473fb2342b 100644 --- a/recipes/ucsc-tolower/meta.yaml +++ b/recipes/ucsc-tolower/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-tolower" %} {% set program = "toLower" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -19,7 +19,6 @@ build: run_exports: - {{ pin_subpackage(package, max_pin=None) }} - requirements: build: - make @@ -44,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert upper case to lower case in file. Leave other chars alone" dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-toupper/build.sh b/recipes/ucsc-toupper/build.sh index d7cbdb9fffac3..ce555e0c80bf6 100644 --- a/recipes/ucsc-toupper/build.sh +++ b/recipes/ucsc-toupper/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/toUpper && make) -cp bin/toUpper "$PREFIX/bin" -chmod +x "$PREFIX/bin/toUpper" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/toUpper && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/toUpper "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/toUpper" diff --git a/recipes/ucsc-toupper/include.patch b/recipes/ucsc-toupper/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-toupper/include.patch +++ b/recipes/ucsc-toupper/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-toupper/meta.yaml b/recipes/ucsc-toupper/meta.yaml index 15c9ce22d1447..321ceb63c29a7 100644 --- a/recipes/ucsc-toupper/meta.yaml +++ b/recipes/ucsc-toupper/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-toupper" %} {% set program = "toUpper" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert lower case to upper case in file. Leave other chars alone" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-transmappsltogenepred/build.sh b/recipes/ucsc-transmappsltogenepred/build.sh index 9dd5385bb891c..5e65bc273c9cc 100644 --- a/recipes/ucsc-transmappsltogenepred/build.sh +++ b/recipes/ucsc-transmappsltogenepred/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/transMapPslToGenePred && make) -cp bin/transMapPslToGenePred "$PREFIX/bin" -chmod +x "$PREFIX/bin/transMapPslToGenePred" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/transMapPslToGenePred && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/transMapPslToGenePred "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/transMapPslToGenePred" diff --git a/recipes/ucsc-transmappsltogenepred/include.patch b/recipes/ucsc-transmappsltogenepred/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-transmappsltogenepred/include.patch +++ b/recipes/ucsc-transmappsltogenepred/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-transmappsltogenepred/meta.yaml b/recipes/ucsc-transmappsltogenepred/meta.yaml index 79d57d1cd27f4..4759a690a0db9 100644 --- a/recipes/ucsc-transmappsltogenepred/meta.yaml +++ b/recipes/ucsc-transmappsltogenepred/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-transmappsltogenepred" %} {% set program = "transMapPslToGenePred" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "convert PSL alignments of mRNAs to gene annotations." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-trfbig/build.sh b/recipes/ucsc-trfbig/build.sh index fa7537a9dec25..cdc8a63b351a6 100644 --- a/recipes/ucsc-trfbig/build.sh +++ b/recipes/ucsc-trfbig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/trfBig && make) -cp bin/trfBig "$PREFIX/bin" -chmod +x "$PREFIX/bin/trfBig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/trfBig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/trfBig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/trfBig" diff --git a/recipes/ucsc-trfbig/include.patch b/recipes/ucsc-trfbig/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-trfbig/include.patch +++ b/recipes/ucsc-trfbig/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-trfbig/meta.yaml b/recipes/ucsc-trfbig/meta.yaml index 828d2326d10e3..0025de973200c 100644 --- a/recipes/ucsc-trfbig/meta.yaml +++ b/recipes/ucsc-trfbig/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-trfbig" %} {% set program = "trfBig" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Mask tandem repeats on a big sequence file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-twobitdup/build.sh b/recipes/ucsc-twobitdup/build.sh index 245b2d099cb46..634c386a90d8d 100644 --- a/recipes/ucsc-twobitdup/build.sh +++ b/recipes/ucsc-twobitdup/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/twoBitDup && make) -cp bin/twoBitDup "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitDup" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/twoBitDup && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitDup "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitDup" diff --git a/recipes/ucsc-twobitdup/include.patch b/recipes/ucsc-twobitdup/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobitdup/include.patch +++ b/recipes/ucsc-twobitdup/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-twobitdup/meta.yaml b/recipes/ucsc-twobitdup/meta.yaml index ceb58f9e80f56..18ea0f188ccfd 100644 --- a/recipes/ucsc-twobitdup/meta.yaml +++ b/recipes/ucsc-twobitdup/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitdup" %} {% set program = "twoBitDup" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "check to see if a twobit file has any identical sequences in it" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-twobitinfo/build.sh b/recipes/ucsc-twobitinfo/build.sh index 5921bddf59576..510984dbad870 100644 --- a/recipes/ucsc-twobitinfo/build.sh +++ b/recipes/ucsc-twobitinfo/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/twoBitInfo && make) -cp bin/twoBitInfo "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitInfo" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/twoBitInfo && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitInfo "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitInfo" diff --git a/recipes/ucsc-twobitinfo/include.patch b/recipes/ucsc-twobitinfo/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobitinfo/include.patch +++ b/recipes/ucsc-twobitinfo/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index 32559085469d0..f02d59ed3bbbe 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitinfo" %} {% set program = "twoBitInfo" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -12,14 +12,10 @@ source: sha256: "{{ sha256 }}" patches: - "include.patch" - - htmshell.patch build: - skip: True # [osx] - number: 1 - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} @@ -27,31 +23,35 @@ requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "get information about sequences in a .2bit file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-twobitmask/build.sh b/recipes/ucsc-twobitmask/build.sh index 5368b1069ee35..04192302896ce 100644 --- a/recipes/ucsc-twobitmask/build.sh +++ b/recipes/ucsc-twobitmask/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/utils/twoBitMask && make) -cp bin/twoBitMask "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitMask" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/utils/twoBitMask && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitMask "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitMask" diff --git a/recipes/ucsc-twobitmask/include.patch b/recipes/ucsc-twobitmask/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobitmask/include.patch +++ b/recipes/ucsc-twobitmask/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-twobitmask/meta.yaml b/recipes/ucsc-twobitmask/meta.yaml index b4712f7ebff1e..cfef8cf9866cd 100644 --- a/recipes/ucsc-twobitmask/meta.yaml +++ b/recipes/ucsc-twobitmask/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-twobitmask" %} {% set program = "twoBitMask" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "apply masking to a .2bit file, creating a new .2bit file" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-twobittofa/build.sh b/recipes/ucsc-twobittofa/build.sh index 8f25dc11367ae..1db3e3360894c 100644 --- a/recipes/ucsc-twobittofa/build.sh +++ b/recipes/ucsc-twobittofa/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" + +set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make -j ${CPU_COUNT}) -(cd kent/src/htslib && make -j ${CPU_COUNT}) -(cd kent/src/jkOwnLib && make -j ${CPU_COUNT}) -(cd kent/src/hg/lib && make -j ${CPU_COUNT}) -(cd kent/src/utils/twoBitToFa && make -j ${CPU_COUNT}) -cp bin/twoBitToFa "$PREFIX/bin" -chmod +x "$PREFIX/bin/twoBitToFa" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/twoBitToFa && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/twoBitToFa "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/twoBitToFa" diff --git a/recipes/ucsc-twobittofa/include.patch b/recipes/ucsc-twobittofa/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-twobittofa/include.patch +++ b/recipes/ucsc-twobittofa/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml index 9469bbbab5f7e..6c74d0cff77f5 100644 --- a/recipes/ucsc-twobittofa/meta.yaml +++ b/recipes/ucsc-twobittofa/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-twobittofa" %} {% set program = "twoBitToFa" %} -{% set version = "455" %} -{% set sha256 = "e458cadad7c4a5c1b8385edafffa1b29380ac725a0c20535bf5a3bab99fe80db" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - skip: True # [osx] - number: 1 - ignore_run_exports: - - libpng - - libuuid + skip: True # [osx] + number: 0 run_exports: - - {{ pin_subpackage("ucsc-twobittofa", max_pin=None) }} + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert all or part of .2bit file to fasta" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-validatefiles/build.sh b/recipes/ucsc-validatefiles/build.sh index d7fc914c34542..59fd038fccaa6 100644 --- a/recipes/ucsc-validatefiles/build.sh +++ b/recipes/ucsc-validatefiles/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/encode3/validateFiles && make) -cp bin/validateFiles "$PREFIX/bin" -chmod +x "$PREFIX/bin/validateFiles" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/encode3/validateFiles && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/validateFiles "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/validateFiles" diff --git a/recipes/ucsc-validatefiles/include.patch b/recipes/ucsc-validatefiles/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-validatefiles/include.patch +++ b/recipes/ucsc-validatefiles/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-validatefiles/meta.yaml b/recipes/ucsc-validatefiles/meta.yaml index 834d239050a73..e0b2c141b8335 100644 --- a/recipes/ucsc-validatefiles/meta.yaml +++ b/recipes/ucsc-validatefiles/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-validatefiles" %} {% set program = "validateFiles" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Validates the format of different genomic files." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-validatemanifest/build.sh b/recipes/ucsc-validatemanifest/build.sh index e727b91ce0514..f92f057e59eaf 100644 --- a/recipes/ucsc-validatemanifest/build.sh +++ b/recipes/ucsc-validatemanifest/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/encode3/validateManifest && make) -cp bin/validateManifest "$PREFIX/bin" -chmod +x "$PREFIX/bin/validateManifest" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/encode3/validateManifest && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/validateManifest "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/validateManifest" diff --git a/recipes/ucsc-validatemanifest/include.patch b/recipes/ucsc-validatemanifest/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-validatemanifest/include.patch +++ b/recipes/ucsc-validatemanifest/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-validatemanifest/meta.yaml b/recipes/ucsc-validatemanifest/meta.yaml index a80b36a6feb4d..a3b17fc4ab953 100644 --- a/recipes/ucsc-validatemanifest/meta.yaml +++ b/recipes/ucsc-validatemanifest/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-validatemanifest" %} {% set program = "validateManifest" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Validates the ENCODE3 manifest.txt file." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-websync/build.sh b/recipes/ucsc-websync/build.sh index f39703618a8ac..eebbd4ce9a700 100644 --- a/recipes/ucsc-websync/build.sh +++ b/recipes/ucsc-websync/build.sh @@ -1,4 +1,7 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -cp kent/src/utils/webSync "$PREFIX/bin" -chmod +x "$PREFIX/bin/webSync" + +set -xe + +mkdir -p "${PREFIX}/bin" +cp kent/src/utils/webSync "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/webSync" diff --git a/recipes/ucsc-websync/include.patch b/recipes/ucsc-websync/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-websync/include.patch +++ b/recipes/ucsc-websync/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-websync/meta.yaml b/recipes/ucsc-websync/meta.yaml index c4bcd00e92eb8..27a97d1a0631c 100644 --- a/recipes/ucsc-websync/meta.yaml +++ b/recipes/ucsc-websync/meta.yaml @@ -1,30 +1,39 @@ {% set package = "ucsc-websync" %} {% set program = "webSync" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" version: "{{ version }}" source: - url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" + url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{ version }.src.tgz" sha256: "{{ sha256 }}" patches: - "include.patch" build: skip: True # [osx] - number: 2 + number: 0 + run_exports: + - { pin_subpackage(package, max_pin=None) } requirements: build: + - {{ compiler('c') }} host: + - libpng + - libuuid + - mysql-connector-c + - libopenssl-static + - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - python - zlib @@ -37,3 +46,12 @@ about: home: "http://hgdownload.cse.ucsc.edu/admin/exe/" license: "varies; see http://genome.ucsc.edu/license" summary: "download from https server, using files.txt on their end to get the list of files" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-wigcorrelate/build.sh b/recipes/ucsc-wigcorrelate/build.sh index dadcd1bb5bb53..716aad0dea677 100644 --- a/recipes/ucsc-wigcorrelate/build.sh +++ b/recipes/ucsc-wigcorrelate/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/wigCorrelate && make) -cp bin/wigCorrelate "$PREFIX/bin" -chmod +x "$PREFIX/bin/wigCorrelate" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/wigCorrelate && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/wigCorrelate "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/wigCorrelate" diff --git a/recipes/ucsc-wigcorrelate/include.patch b/recipes/ucsc-wigcorrelate/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-wigcorrelate/include.patch +++ b/recipes/ucsc-wigcorrelate/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-wigcorrelate/meta.yaml b/recipes/ucsc-wigcorrelate/meta.yaml index 691ade53701fd..dfa59e07f8970 100644 --- a/recipes/ucsc-wigcorrelate/meta.yaml +++ b/recipes/ucsc-wigcorrelate/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-wigcorrelate" %} {% set program = "wigCorrelate" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Produce a table that correlates all pairs of wigs." + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-wigtobigwig/build.sh b/recipes/ucsc-wigtobigwig/build.sh index f150228de66bc..113f9a2031ecb 100644 --- a/recipes/ucsc-wigtobigwig/build.sh +++ b/recipes/ucsc-wigtobigwig/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/wigToBigWig && make) -cp bin/wigToBigWig "$PREFIX/bin" -chmod +x "$PREFIX/bin/wigToBigWig" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/wigToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/wigToBigWig "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/wigToBigWig" diff --git a/recipes/ucsc-wigtobigwig/include.patch b/recipes/ucsc-wigtobigwig/include.patch index e9c8621194325..edc04d0dc2f64 100644 --- a/recipes/ucsc-wigtobigwig/include.patch +++ b/recipes/ucsc-wigtobigwig/include.patch @@ -1,30 +1,22 @@ --- kent/src/inc/common.mk 2017-11-07 17:46:00.000000000 -0500 -+++ kent/src/inc/common.mk 2017-11-13 17:44:51.017090255 -0500 ++++ kent/src/inc/common.mk.new 2017-11-13 17:44:51.017090255 -0500 @@ -17,7 +17,7 @@ endif HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -+++ kent/src/inc/common.mk 2022-10-25 12:00:00.000000000 +0100 -@@ -147,4 +147,4 @@ -- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl -+ L+=${PREFIX}/lib/libssl.so ${PREFIX}/lib/libcrypto.so -ldl - else - ifneq ($(wildcard /opt/local/lib/libssl.a),) - L+=/opt/local/lib/libssl.a ---- kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 -+++ kent/src/hg/lib/straw/makefile 2022-10-26 12:00:00.000000000 +0100 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ --KENT_INC=-I../../../inc -+KENT_INC=-I../../../inc -I${PREFIX}/include - - straw: straw.o cStraw.o - ld -r -o ../straw.o straw.o cStraw.o +-#!/usr/bin/env python2.7 ++#!/usr/bin/env python + + import logging, sys, optparse, string + from collections import defaultdict --- kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 +++ kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml index c21b3a9bb7d40..ac2226d78ed5d 100644 --- a/recipes/ucsc-wigtobigwig/meta.yaml +++ b/recipes/ucsc-wigtobigwig/meta.yaml @@ -1,57 +1,57 @@ {% set package = "ucsc-wigtobigwig" %} {% set program = "wigToBigWig" %} -{% set version = "447" %} -{% set sha256 = "747a48486f7481d891e297baf63623b15d699265ede7339f654bcbc42481ac81" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: - name: {{ package }} - version: {{ version }} + name: "{{ package }}" + version: "{{ version }}" source: url: "http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v{{ version }}.src.tgz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" patches: - - include.patch - - htmshell.patch + - "include.patch" build: - number: 2 - skip: True # [osx] + skip: True # [osx] + number: 0 run_exports: - {{ pin_subpackage(package, max_pin=None) }} - ignore_run_exports: - - libpng - - libuuid requirements: build: - make - {{ compiler('c') }} - - {{ compiler('cxx') }} - - binutils # [linux] host: - libpng - libuuid - mysql-connector-c - - openssl - libopenssl-static - zlib + run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static + - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" - summary: "Convert ascii format wig file (in fixedStep, variableStep)" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" + summary: "Convert ascii format wig file (in fixedStep, variableStep" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-wordline/build.sh b/recipes/ucsc-wordline/build.sh index 2986588d188dc..f9483c43c25ce 100644 --- a/recipes/ucsc-wordline/build.sh +++ b/recipes/ucsc-wordline/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/utils/wordLine && make) -cp bin/wordLine "$PREFIX/bin" -chmod +x "$PREFIX/bin/wordLine" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/utils/wordLine && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/wordLine "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/wordLine" diff --git a/recipes/ucsc-wordline/include.patch b/recipes/ucsc-wordline/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-wordline/include.patch +++ b/recipes/ucsc-wordline/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-wordline/meta.yaml b/recipes/ucsc-wordline/meta.yaml index 340ea0ab85173..a4f886851f2d7 100644 --- a/recipes/ucsc-wordline/meta.yaml +++ b/recipes/ucsc-wordline/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-wordline" %} {% set program = "wordLine" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "chop up words by white space and output them with one" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64 diff --git a/recipes/ucsc-xmlcat/build.sh b/recipes/ucsc-xmlcat/build.sh index 0c43ba87a8e5e..8809a785168a9 100644 --- a/recipes/ucsc-xmlcat/build.sh +++ b/recipes/ucsc-xmlcat/build.sh @@ -1,21 +1,21 @@ #!/bin/bash set -xe + +mkdir -p "${PREFIX}/bin" export MACHTYPE=$(uname -m) +export BINDIR=$(pwd)/bin export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 -export BINDIR=$(pwd)/bin export L="${LDFLAGS}" -mkdir -p "$BINDIR" +mkdir -p "${BINDIR}" (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") (cd kent/src/hg/xmlCat && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") -cp -f bin/xmlCat "$PREFIX/bin" -chmod 0755 "$PREFIX/bin/xmlCat" +cp bin/xmlCat "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/xmlCat" diff --git a/recipes/ucsc-xmlcat/meta.yaml b/recipes/ucsc-xmlcat/meta.yaml index f7728bd133b59..fdfb1b545ec90 100644 --- a/recipes/ucsc-xmlcat/meta.yaml +++ b/recipes/ucsc-xmlcat/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-xmlcat" %} {% set program = "xmlCat" %} -{% set version = "466" %} -{% set sha256 = "5ed312771de13b18a72f3f3f615ef1bc0b8be9dcd647b8dde05dc60d4630e9fb" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -43,12 +43,15 @@ test: - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Concatenate xml files together, stuffing all records inside a single outer tag. " dev_url: "https://github.com/ucscGenomeBrowser/kent" doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 diff --git a/recipes/ucsc-xmltosql/build.sh b/recipes/ucsc-xmltosql/build.sh index 9c0109eec1bf3..da748dca33f72 100644 --- a/recipes/ucsc-xmltosql/build.sh +++ b/recipes/ucsc-xmltosql/build.sh @@ -1,13 +1,21 @@ #!/bin/bash -mkdir -p "$PREFIX/bin" -export MACHTYPE=x86_64 + +set -xe + +mkdir -p "${PREFIX}/bin" +export MACHTYPE=$(uname -m) export BINDIR=$(pwd)/bin +export INCLUDE_PATH="${PREFIX}/include" +export LIBRARY_PATH="${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" +export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}" export L="${LDFLAGS}" -mkdir -p "$BINDIR" -(cd kent/src/lib && make) -(cd kent/src/htslib && make) -(cd kent/src/jkOwnLib && make) -(cd kent/src/hg/lib && make) -(cd kent/src/hg/xmlToSql && make) -cp bin/xmlToSql "$PREFIX/bin" -chmod +x "$PREFIX/bin/xmlToSql" +mkdir -p "${BINDIR}" +(cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +(cd kent/src/hg/xmlToSql && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}") +cp bin/xmlToSql "${PREFIX}/bin" +chmod 0755 "${PREFIX}/bin/xmlToSql" diff --git a/recipes/ucsc-xmltosql/include.patch b/recipes/ucsc-xmltosql/include.patch index eb32b88d8f358..edc04d0dc2f64 100644 --- a/recipes/ucsc-xmltosql/include.patch +++ b/recipes/ucsc-xmltosql/include.patch @@ -5,12 +5,12 @@ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I ${PREFIX}/include ++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I${kentSrc}/htslib -I${PREFIX}/include -I${BUILD_PREFIX}/include # to check for Mac OSX Darwin specifics: UNAME_S := $(shell uname -s) ---- kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 -+++ kent/src/utils/bedJoinTabOffset 2018-06-06 02:23:56.000000000 +0200 +--- kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 ++++ kent/src/utils/bedJoinTabOffset.py 2018-06-06 02:23:56.000000000 +0200 @@ -1,4 +1,4 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python diff --git a/recipes/ucsc-xmltosql/meta.yaml b/recipes/ucsc-xmltosql/meta.yaml index e73be12d74a2d..d66247fc304ce 100644 --- a/recipes/ucsc-xmltosql/meta.yaml +++ b/recipes/ucsc-xmltosql/meta.yaml @@ -1,7 +1,7 @@ {% set package = "ucsc-xmltosql" %} {% set program = "xmlToSql" %} -{% set version = "377" %} -{% set sha256 = "932f149c19641064a9cd3f2382cbb54b45a9292b8444792872d531346925d676" %} +{% set version = "469" %} +{% set sha256 = "3f95b26ccca854c965c05773481c269f2a0e6fb1906ae8a7fe2437c6ad543963" %} package: name: "{{ package }}" @@ -15,7 +15,9 @@ source: build: skip: True # [osx] - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage(package, max_pin=None) }} requirements: build: @@ -25,22 +27,31 @@ requirements: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib run: - libpng - libuuid - mysql-connector-c - - openssl + - libopenssl-static - zlib test: commands: - # just check for existence, because the individual packages have no unified behavior - - which {{ program }} + # just check for existence and exec bit, because the individual packages have no unified behavior + - test -x ${PREFIX}/bin/{{ program }} about: - home: "http://hgdownload.cse.ucsc.edu/admin/exe/" - license: "varies; see http://genome.ucsc.edu/license" + home: "https://hgdownload.cse.ucsc.edu/admin/exe/" + license: "Varies; see http://genome.ucsc.edu/license" summary: "Convert XML dump into a fairly normalized relational database" + dev_url: "https://github.com/ucscGenomeBrowser/kent" + doc_url: "https://github.com/ucscGenomeBrowser/kent/blob/master/README" + +extra: + identifiers: + - biotools:UCSC_Genome_Browser_Utilities + - doi:10.1093/bib/bbs038 + additional-platforms: + - linux-aarch64