bulk update latest ucsc version and fix failures

bioconda · Aug 27, 2024 · 636e3f0 · 636e3f0
1 parent b7bc2f5
commit 636e3f0
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diff --git 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
@@ -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
+    - linux-aarch64
diff --git 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
@@ -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
@@ -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
@@ -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
+    - linux-aarch64
diff --git 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
@@ -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
@@ -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
@@ -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
+    - linux-aarch64
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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