Merge branch 'bioconda:master' into master

bioconda · Nov 12, 2024 · 4945f34 · 4945f34
2 parents 8e4b34c + d29672a
commit 4945f34
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diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml
@@ -1,17 +1,17 @@
-{% set version = "1.2.7" %}
+{% set version = "1.2.8" %}
 
 package:
   name: arcs
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('arcs', max_pin="x") }}
 
 source:
   url: https://github.com/bcgsc/arcs/releases/download/v{{ version }}/arcs-{{ version }}.tar.gz
-  sha256: 3162cff3286a033b494ace8050abc96d4083f846cafe921bb0122170f705eca8
+  sha256: 3393151980ee1e031ff47d32e2871745255a08e9e76f27657e868137b4ddd2df
 
 requirements:
   build:
@@ -43,4 +43,4 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
-    - osx-arm64
+    - osx-arm64
diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "argo" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253
+  sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ build:
 requirements:
   host:
     - pip
+    - setuptools
     - python >=3.7
   run:
     - python >=3.7
@@ -36,7 +37,7 @@ about:
   home: https://github.com/xinehc/argo
   license: MIT
   license_family: MIT
-  summary: 'Argo: species-resolved profiling of antibiotic resistant genes with long-read metagenomics'
+  summary: 'Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping'
 
 extra:
   recipe-maintainers:

diff --git a/recipes/argparse2tool/meta.yaml b/recipes/argparse2tool/meta.yaml
@@ -1,28 +1,30 @@
 {% set name = "argparse2tool" %}
-{% set version = "0.4.9" %}
+{% set version = "0.5.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: ecd7142c1ce60bf9e1416443ce393907b7f99a9396a0530277c110dcb7106579
+  sha256: 8c6fbf68df690edf80f438b458e6da1f943254b0c4337ac2b732c567c67fde46
 
 build:
   number: 0
   entry_points:
     - argparse2tool_check_path = argparse2tool.check_path:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
+  run_exports:
+    - {{ pin_subpackage('argparse2tool', max_pin="x.x") }}
 
 requirements:
   host:
     - pip
     - python >=3
+    - setuptools
   run:
-    - click
-    - galaxyxml >=0.2.3
+    - galaxyxml >=0.4.6
     - jinja2
     - python >=3
 

diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh
@@ -7,7 +7,7 @@ mkdir -p $GEM_HOME
 gem build aspera-cli.gemspec
 gem install --install-dir $GEM_HOME --bindir $GEM_HOME/bin ${PKG_NAME}-${PKG_VERSION}.gem
 gem_path=$GEM_HOME/gems/${PKG_NAME}-${PKG_VERSION}
-cp -r $SRC_DIR/* $gem_path
+cp -rf $SRC_DIR/* $gem_path
 rm $gem_path/{conda_build,build_env_setup}.sh
 tail -n+3 bin/ascli > $gem_path/bin/ascli
 tail -n+3 bin/asession > $gem_path/bin/asession
@@ -25,9 +25,6 @@ EOF
 echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli
 echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession
 
-ln -s $gem_path/bin/* $PREFIX/bin
+ln -sf $gem_path/bin/* $PREFIX/bin
 
-export ASCLI_HOME="$PREFIX/etc/aspera"
-ascli conf ascp install && ascli config ascp info 
-cp $ASCLI_HOME/aspera-license .
-ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin
+ascli conf ascp install && ascli config ascp info
diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml
@@ -1,23 +1,21 @@
 {% set name = "aspera-cli" %}
-{% set version = "4.14.0" %}
+{% set version = "4.19.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-    sha256: b46df368df71ad926605e85ea4b61b9e48335cce8be31ac04d97ee6f71109f03
+    sha256: e4f9eb47510094132ff02960764254dfc322f1a16c9ad2b8abc60a54e5e21da1
 
 build:
   noarch: generic
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('aspera-cli', max_pin="x") }}
 
 requirements:
-  build:
-    - ruby >=3
   host:
     - ruby >=3
   run:
@@ -26,16 +24,15 @@ requirements:
 test:
   commands:
     - ascli -h
-    - ascp -h
 
 about:
-  home: https://github.com/IBM/aspera-cli
-  license: Apache-2.0
-  license_file: 
-    - LICENSE
-    - aspera-license
-  summary: "Command Line Interface for IBM Aspera products"
-  dev_url: https://github.com/IBM/aspera-cli
+  home: "https://github.com/IBM/aspera-cli"
+  license: "Apache-2.0"
+  license_file: LICENSE
+  license_family: APACHE
+  summary: "Command Line Interface for IBM Aspera products."
+  dev_url: "https://github.com/IBM/aspera-cli"
+  doc_url: "https://www.rubydoc.info/gems/aspera-cli"
 
 extra:
   recipe-maintainers:

diff --git a/recipes/bam2plot/meta.yaml b/recipes/bam2plot/meta.yaml
@@ -0,0 +1,48 @@
+{% set name = "bam2plot" %}
+{% set version = "0.3.6" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz
+  sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541
+
+build:
+  entry_points:
+    - bam2plot=bam2plot.main:cli
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('bam2plot', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - setuptools
+  run:
+    - python >=3.10
+    - pysam >=0.22.0
+    - seaborn >=0.13.2
+    - polars >=0.20.15
+    - mappy >=2.28
+    - pyfastx
+    - pyarrow
+    - mosdepth
+
+test:
+  imports:
+    - bam2plot
+  commands:
+    - bam2plot from_bam --help
+    - bam2plot from_reads --help
+    - bam2plot guci --help
+
+about:
+  home: https://github.com/willros/bam2plot
+  summary: Plot of coverage from bam file
+  license: GPL-3.0-only
+  license_file: LICENSE
diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "BBMap" %}
-{% set version = "39.10" %}
-{% set sha256 = "996aff05765ba5e64547f8a34c56da396ce7b18db96ffe7f1076f2d2f49c6148" %}
+{% set version = "39.11" %}
+{% set sha256 = "bcb80b109757a638d6c767b7ba785fde5111437f7025e0a93dce587cdfaa2795" %}
 
 package:
   name: {{ name|lower }}
@@ -19,13 +19,13 @@ requirements:
   build:
     - {{ compiler('c') }}
   host:
-    - openjdk >=7.0
+    - openjdk >=11.0.1
     - pbzip2
     - bzip2
     - samtools
     - patchelf  # [osx]
   run:
-    - openjdk >=7.0
+    - openjdk >=11.0.1
     - samtools
 
 test:

diff --git a/recipes/bftools/meta.yaml b/recipes/bftools/meta.yaml
@@ -1,18 +1,20 @@
-{% set version = "6.7.0" %}
-{% set sha256 = "7c013b23529d61280e04c3dd312401d7b71fb5892f5e7870f87d37bab5f3988f" %}
+{% set version = "8.0.0" %}
+{% set sha256 = "46c7c53595a2491adc76dc3b7d4089689e5c3817a9bb549a632d08ef137438e7" %}
 
 
 package:
   name: bftools
   version: '{{version}}'
 
 source:
-  url: "http://downloads.openmicroscopy.org/latest/bio-formats{{version}}/artifacts/bftools.zip"
+  url: https://downloads.openmicroscopy.org/bio-formats/{{ version }}/artifacts/bftools.zip
   sha256: '{{sha256}}'
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('bftools', max_pin="x.x") }}
 
 requirements:
   run:
@@ -21,6 +23,8 @@ requirements:
 test:
   commands:
     - bfconvert -version
+    - domainlist
+    - formatlist
 
 about:
   home: https://docs.openmicroscopy.org/bio-formats/{{version}}/users/comlinetools/index.html

diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "biobb_chemistry" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: c4f3926a8a219410afa1e79feb84b71a2d1bb70bc0700039d52726853113b0e8
+  sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
@@ -22,13 +22,13 @@ requirements:
     - setuptools
     - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools >=22.5
+    - ambertools ==22.5
     - acpype >=2023.10.27
   run:
     - python >=3.9
     - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools >=22.5
+    - ambertools ==22.5
     - acpype >=2023.10.27
 test:
   imports:

diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bioblend" %}
-{% set version = "1.3.0" %}
+{% set version = "1.4.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz
-  sha256: e72318e10c29a81c16281d25aaac00989a07fc2900be7479137964232cc4a507
+  sha256: 175d49d288e27d132ff59c870551c87cd95d7747be55ab94807c563291a3fa1d
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - requests >=2.20.0
@@ -66,7 +67,7 @@ test:
 about:
   home: "https://github.com/galaxyproject/bioblend"
   license: MIT
-  summary: 'A Python library for interacting with the Galaxy API'
+  summary: 'A Python library for interacting with the Galaxy API.'
   license_family: MIT
   license_file: LICENSE
   doc_url: "https://bioblend.readthedocs.org/"

diff --git a/recipes/cat/build.sh b/recipes/cat/build.sh
@@ -6,7 +6,6 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 mkdir -p $outdir
 mkdir -p $PREFIX/bin
 
-
 mv CAT_pack $outdir
 
-ln -s $outdir/CAT_pack/CAT $PREFIX/bin
+ln -s $outdir/CAT_pack/CAT_pack $PREFIX/bin
diff --git a/recipes/cat/meta.yaml b/recipes/cat/meta.yaml
@@ -1,32 +1,35 @@
-{% set version = "5.3" %}
-{% set sha256 = "2893ee18b0d5b24a291edd7d8ca1738d40ea189d18ba0fb7aad3e38973a787e7" %}
+{% set version = "6.0.1" %}
+{% set sha256 = "189707d8a0f6fa3ce50ed5fd5e9955b97119b514d38a190d393a701ec652f8fc" %}
 
 package:
   name: cat
   version: {{ version }}
 
 source:
-  url: https://github.com/dutilh/CAT/archive/v{{ version }}.tar.gz
+  url: https://github.com/MGXlab/CAT_pack/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }} 
 
 build:
   number: 0
   noarch: generic
   run_exports:
     - {{ pin_subpackage("cat", max_pin="x") }}
+
 requirements:
   run:
-    - python 3
+    - python >=3
     - diamond
     - prodigal
 
 test:
   commands:
-    - CAT prepare --help
+    - CAT_pack prepare -h
 
 about:
   summary: |
     CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
-  home: https://github.com/dutilh/CAT
+  home: https://github.com/MGXlab/CAT_pack
   license: MIT
+  license_family: MIT
   license_file: LICENSE.md
+  dev_url: https://github.com/MGXlab/CAT_pack