Merge branch 'master' into bulk

bioconda · Jun 13, 2024 · 0dc4f5e · 0dc4f5e
2 parents d69bb40 + 1fd2229
commit 0dc4f5e
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -764,15 +764,13 @@ recipes/conterminator
 recipes/mantis
 recipes/apoc
 recipes/quorum
-recipes/curves
 recipes/noresm
 recipes/xsd
 recipes/callstate
 recipes/hypo
 recipes/pb-falcon-phase
 recipes/hiline
 recipes/eqtlbma
-recipes/selene-sdk
 recipes/barriers
 
 # Requires rmblast update
@@ -782,20 +780,11 @@ recipes/maker
 recipes/rop
 
 # Need to redo the skeletons for these
-recipes/ucsc-addcols
-recipes/ucsc-ameme
-recipes/ucsc-autodtd
-recipes/ucsc-autosql
-recipes/ucsc-autoxml
-recipes/ucsc-avecols
-recipes/ucsc-axtsort
 recipes/ucsc-axtswap
 recipes/ucsc-axttomaf
 recipes/ucsc-bamtopsl
-recipes/ucsc-bedcommonregions
 recipes/ucsc-bedcoverage
 recipes/ucsc-bedextendranges
-recipes/ucsc-bedgeneparts
 recipes/ucsc-bedgraphpack
 recipes/ucsc-bedintersect
 recipes/ucsc-beditemoverlapcount
@@ -807,17 +796,6 @@ recipes/ucsc-bedsort
 recipes/ucsc-bedtogenepred
 recipes/ucsc-bedtopsl
 recipes/ucsc-bedweedoverlapping
-recipes/ucsc-bigbedinfo
-recipes/ucsc-bigbednameditems
-recipes/ucsc-bigbedsummary
-recipes/ucsc-bigbedtobed
-recipes/ucsc-bigmaftomaf
-recipes/ucsc-bigpsltopsl
-recipes/ucsc-bigwigaverageoverbed
-recipes/ucsc-bigwigcat
-recipes/ucsc-bigwigcluster
-recipes/ucsc-bigwigcorrelate
-recipes/ucsc-bigwiginfo
 recipes/ucsc-bigwigmerge
 recipes/ucsc-blasttopsl
 recipes/ucsc-catdir
@@ -875,7 +853,6 @@ recipes/ucsc-genepredfilter
 recipes/ucsc-genepredhisto
 recipes/ucsc-genepredsinglecover
 recipes/ucsc-genepredtofakepsl
-recipes/ucsc-genepredtogtf
 recipes/ucsc-genepredtomafframes
 recipes/ucsc-genepredtoprot
 recipes/ucsc-gensub2

diff --git a/recipes/abnumber/meta.yaml b/recipes/abnumber/meta.yaml
@@ -1,15 +1,17 @@
-{% set version = "0.3.2" %} # Remember to update sha256 below
+{% set version = "0.3.5" %} # Remember to update sha256 below
 
 package:
   name: abnumber
   version: '{{ version }}'
 
 source:
   url: https://github.com/prihoda/abnumber/archive/v{{ version }}.tar.gz
-  sha256: '1e00d010a05b2b7fe93660346f8b0bc36d7058e2655c3f779d84c85b52022ebc'
+  sha256: '6fb14c90c071306b3d87484242bb5e8e89ba4c1bb45461d64a9b1b6bc415bbdb'
 
 build:
   noarch: python
+  run_exports:
+    - {{ pin_subpackage('abnumber', max_pin="x.x") }}
   number: 0
   script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv
 

diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.37.0" %}
+{% set version = "0.38.0" %}
 
 package:
   name: annonars
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 07fcf371b876b934111bd9c8d3ffe37bf834d7a9661b1ca1c7e93ce663e56feb
+  sha256: 744115fa199e798760adaa7f5a6d8c7f1a4976785456e9557fd6f1cc39e78612
 
 requirements:
   build:

diff --git a/recipes/argnorm/meta.yaml b/recipes/argnorm/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "argnorm" %}
-{% set version = "0.3.0" %}
+{% set version = "0.4.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 32ae41d1c099558b3257f88dd5ff34e70614646dec5bbf6fd7e0b30f816a5f57
+  sha256: 9144013b7e1f5eb32abeb90281ba8cc1653272a0208d1167268a55440163a72a
 
 build:
   noarch: python

diff --git a/recipes/assemblycomparator2/build.sh b/recipes/assemblycomparator2/build.sh
@@ -7,8 +7,8 @@ export PACKAGE_HOME="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
 # First we put the necessary files in into the conda prefix/share directory:
 mkdir -p "${PACKAGE_HOME}"
 chmod 755 asscom2
-cp -f asscom2 workflow/Snakefile config/config.yaml "${PACKAGE_HOME}"
-cp -rf docs profile workflow/scripts tests "${PACKAGE_HOME}"
+cp -f asscom2 LICENSE "${PACKAGE_HOME}"
+cp -rf config docs dynamic_report profile resources tests workflow "${PACKAGE_HOME}"
 
 # This is the binary that we wish to be able to run.
 ln -sf ${PACKAGE_HOME}/asscom2 ${PREFIX}/bin/asscom2
diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml
@@ -11,30 +11,30 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 2
   noarch: generic
   run_exports:
     - {{ pin_subpackage('assemblycomparator2', max_pin="x") }}
 
 requirements:
   run:
-    - python >=3.11
     - snakemake-minimal <8
     - pulp <2.8
-    - mamba >=1.5.8  # Necessary for snakemake to install child environments during development.
+    - mamba # Necessary for snakemake to install child environments during development.
+    - pandas
 
 test:
   commands:
     - "touch dummy.fa; asscom2 --help"
 
 about:
   home: "https://github.com/cmkobel/assemblycomparator2"
-  summary: 'assemblycomparator2: Compare prokaryotic genomic assemblies'
+  summary: 'Assemblycomparator2: Genomes to report pipeline'
   license_family: GPL3
   license: "GPL-3.0-or-later"
   license_file: LICENSE
   dev_url: "https://github.com/cmkobel/assemblycomparator2"
-  doc_url: "https://assemblycomparator2.readthedocs.io/en/latest"
+  doc_url: "https://assemblycomparator2.readthedocs.io/"
 
 extra:
   recipe-maintainers:

diff --git a/recipes/auspice/build.sh b/recipes/auspice/build.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
-set -euo pipefail
+set -xeuo pipefail
 
 mkdir -p $PREFIX/lib/auspice
 pushd $PREFIX/lib/auspice

diff --git a/recipes/auspice/meta.yaml b/recipes/auspice/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.52.0" %}
+{% set version = "2.54.1" %}
 
 package:
   name: auspice
   version: {{ version }}
 
 source:
   url: https://registry.npmjs.org/auspice/-/auspice-{{ version }}.tgz
-  sha256: c23a411c10066d173ed2c4b687e3f60429b3ef4cf16cc6e13d79766bafba28df
+  sha256: 67533ac3545089f200ef44598ab12d4a937b7018cc8c4c192e0516ab6081731b
 
 build:
   number: 0
@@ -23,6 +23,8 @@ requirements:
     - python *
     - pkg-config
     - yarn 1.*
+  host:
+    - icu
   run:
     - nodejs 16.*|18.*|20.*
 
@@ -35,11 +37,13 @@ about:
   doc_url: https://docs.nextstrain.org/projects/auspice/
   dev_url: https://github.com/nextstrain/auspice
   summary: Auspice is an open-source interactive tool for visualising phylogenomic data
-  license: AGPL-3.0
+  license: AGPL-3.0-only
   license_file: LICENSE.txt
   license_family: AGPL
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - jameshadfield
     - victorlin

diff --git a/recipes/bamread/meta.yaml b/recipes/bamread/meta.yaml
@@ -10,10 +10,10 @@ source:
   sha256: 913ae7d433592aa9bfad8699da93e74b5dfe8f567a1ebf4147f0da61baaf2b70
 
 build:
-  number: 3
-  run_exports:
-    - {{ pin_subpackage("bamread", max_pin="x.x.x") }}
+  number: 4
   script: python setup.py install --single-version-externally-managed --record=record.txt
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   build:
@@ -41,5 +41,7 @@ about:
   summary: Read bam files quickly into dataframes in Python
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   skip-lints:
     - uses_setuptools
diff --git a/recipes/bamsurgeon/meta.yaml b/recipes/bamsurgeon/meta.yaml
@@ -0,0 +1,44 @@
+{% set name = "Bamsurgeon" %}
+{% set version = "1.4.1" %}
+
+package:
+  name: '{{ name|lower }}'
+  version: '{{ version }}'
+
+source:
+  url: https://github.com/adamewing/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
+  sha256: 137981f16df21fe5b4f602c641372a20643a8bb92e6c6dddace499427417213f
+  patches:
+    - pyproject.patch
+
+build:
+  run_exports:
+    - {{ pin_subpackage('bamsurgeon', max_pin="x") }}
+  script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed --no-cache-dir -vvv ."
+  number: 0
+  noarch: python
+
+requirements:
+  host:
+    - python >=3.6
+    - pip
+  run:
+    - python >=3.6
+    - samtools >=1.2
+    - bwa >=0.7.12
+    - exonerate >=2.2
+    - velvet >=1.2
+    - wgsim >=0.2
+    - pysam
+    - picard
+
+test:
+  commands:
+    - addsv.py -h
+    - addsnv.py -h
+    - addindel.py -h
+about:
+  home: https://github.com/adamewing/bamsurgeon
+  license: MIT-license
+  license_file: LICENSE.txt
+  summary: Tools for adding genomic variants to BAM/SAM/CRAM files. Can be used to test variant callers.
diff --git a/recipes/bamsurgeon/pyproject.patch b/recipes/bamsurgeon/pyproject.patch
@@ -0,0 +1,38 @@
+new file mode 100644
+--- /dev/null
++++ pyproject.toml
+@@ -0,0 +1,34 @@
++[build-system]
++requires = ["setuptools>=61.0"]
++build-backend = "setuptools.build_meta"
++
++[project]
++name = "bamsurgeon"
++description = "Tools for adding mutations to existing bam files, used for testing mutation callers"
++readme = "README.md"
++requires-python = ">=3.6"
++license = {file = "LICENSE.txt"}
++classifiers = [
++    "License :: OSI Approved :: MIT License",
++    "Programming Language :: Python :: 3",
++    "Topic :: Scientific/Engineering",
++    "Topic :: Scientific/Engineering :: Bio-Informatics",
++    "Intended Audience :: Science/Research",
++    "Natural Language :: English",
++]
++dependencies = []
++version = "1.4.1"
++
++[project.urls]
++"Homepage" = "https://github.com/adamewing/bamsurgeon"
++
++[tool.setuptools]
++script-files = [
++    "bin/addindel.py",
++    "bin/addsnv.py",
++    "bin/addsv.py"
++]
++
++[tool.setuptools.packages.find]
++where = ["bin"]
++
diff --git a/recipes/bbknn/meta.yaml b/recipes/bbknn/meta.yaml
@@ -10,8 +10,7 @@ source:
   sha256: 1c01a9d6df2fc52a527de8a403617897a4b672724863299a7026f2132f1b041b 
 
 build:
-  number: 1
-  skip: true  # [py2k]
+  number: 2
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv "
   run_exports:
     - {{ pin_subpackage('bbknn', max_pin="x") }}
@@ -53,5 +52,7 @@ about:
   summary: Batch balanced KNN
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - jenzopr
diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.10.5" %}
+{% set version = "0.11.0" %}
 {% set name = "binchicken" %}
-{% set sha256 = "687430f21caba05f654c6ebd26147c9130265de4cfc49d5233d0bcf9fcb07162" %}
+{% set sha256 = "2494f388ac0634341ba6f844df5e35fb30808ad50695016165fc7f88228de179" %}
 
 package:
   name: binchicken

diff --git a/recipes/biobb_model/meta.yaml b/recipes/biobb_model/meta.yaml
@@ -1,8 +1,8 @@
 {% set name = "biobb_model" %}
-{% set version = "4.2.0" %}
+{% set version = "4.2.3" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "99d12334c8aea80adec16e41cb95d03b3fe7e847f94371be4452bf4b3fe09257" %}
+{% set hash_value = "8c4b87ef92331d060700e5b346cddb718b1cc27b79752b1c8ef3583e0dce0927" %}
 
 package:
   name: '{{ name|lower }}'

diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.3.0" %}
-{% set sha256 = "c21f3c75993b00793feb703be80d6c0f8bb34e04f3a4042e007941fe7f156406" %}
+{% set version = "3.3.1" %}
+{% set sha256 = "db6b99456a334b958ba61fcfc6e717e5f22848342f99fecb1f6f2b0113165054" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/bowtie2/build.sh b/recipes/bowtie2/build.sh
@@ -8,7 +8,7 @@ git clone https://github.com/ch4rr0/libsais third_party/libsais
 LDFLAGS=""
 make CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3" CPP="${CXX} -I${PREFIX}/include" CC="${CC} -L${PREFIX}/lib" \
 	CFLAGS="${CFLAGS} -O3" LDLIBS="-L$PREFIX/lib -lz -lzstd -ltbb -ltbbmalloc -lpthread" \
-	WITH_ZSTD=1 USE_SAIS=1
+	WITH_ZSTD=1 USE_SAIS_OPENMP=1
 
 binaries="\
 bowtie2 \
@@ -31,3 +31,5 @@ done
 for d in $directories; do
     cp -rf $d ${PREFIX}/bin
 done
+
+make clean
diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml
@@ -10,7 +10,7 @@ source:
   sha256: 841a6a60111b690c11d1e123cb5c11560b4cd1502b5cee7e394fd50f83e74e13
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('bowtie2', max_pin="x") }}
 
@@ -30,7 +30,8 @@ requirements:
   run:
     - python
     - perl
-    - tbb
+    - llvm-openmp  # [osx]
+    - libgomp  # [linux]
 
 test:
   commands: