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Merge branch 'master' into myloasm-bump
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‎recipes/cesar/meta.yaml‎

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@@ -1,32 +1,39 @@
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{% set version = "1.01" %} # Remember to update sha256 below
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{% set version = "1.02" %}
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package:
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name: cesar
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version: {{ version }}
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source:
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url: https://github.com/hillerlab/CESAR2.0/archive/refs/tags/1.01.tar.gz
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sha256: c85b9529a10c9123f2ab8665606e2ad8d5a1664caf14df7bd2acd8900b79b8d6
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url: https://github.com/hillerlab/CESAR2.0/archive/refs/tags/{{ version }}.tar.gz
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sha256: 62d4615c1a0e5494d4bc7bbda5799bc9f9e04cebc81cd655644bb18d19bed242
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build:
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number: 3
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number: 0
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run_exports:
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- {{ pin_subpackage('cesar', max_pin="x") }}
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requirements:
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build:
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- make
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- {{ compiler('c') }}
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- {{ compiler('cxx') }}
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run:
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test:
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commands:
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- cesar -h 2>&1 | cat > /dev/null
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about:
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home: https://github.com/hillerlab/CESAR2.0
25-
license: MIT license
27+
home: "https://github.com/hillerlab/CESAR2.0"
28+
license: MIT
29+
license_family: MIT
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license_file: LICENSE
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summary: |
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CESAR 2.0 is a method to realign coding exons or genes to DNA sequences using a Hidden Markov Model
31+
summary: "CESAR 2.0 is a method to realign coding exons or genes to DNA sequences using a Hidden Markov Model."
32+
dev_url: "https://github.com/hillerlab/CESAR2.0"
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test:
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commands:
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- cesar -h 2>&1 | cat > /dev/null
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extra:
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skip-lints:
36+
- compiler_needs_stdlib_c
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additional-platforms:
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- linux-aarch64
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- osx-arm64

‎recipes/entrez-direct/build.sh‎

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@@ -5,13 +5,12 @@ set -uex
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mkdir -p bin nobin
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# Don't install these most bespoke scripts
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mv custom-* idx-* pm-* xy-* nobin
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mv xy-* nobin
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# Move ordinary scripts into a subdirectory for convenience
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mv $(find * -type d -prune -o -print | sed '/^[A-Z]/d;/[.]pdf$/d;/[.]pem$/d;/[.]py$/d;/conda/d;/build/d') bin
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mkdir -p $PREFIX/bin
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(cd cmd && sh -ex ./build.sh $PREFIX/bin)
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(cd extern && sh -ex ./build.sh $PREFIX/bin)
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# Ensure conda-build can tidy up this compiler cache tree
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test -d gopath && chmod -R u+wX gopath

‎recipes/entrez-direct/meta.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -1,24 +1,25 @@
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{% set name = "entrez-direct" %}
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{% set version = "24.0" %}
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{% set date = "20250527" %}
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{% set sha256 = "eb5ac6b1faf33a39cc5b2b2eaa2b6ce5e1c05ac3d00d1be2b70bd6054c44f694" %}
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{% set version = "25.3" %}
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{% set date = "20260410" %}
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{% set sha256 = "189382f1fe4a1b43872855cd5b442ed25111192dd4b00330268c1cad6d7216bf" %}
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/edirect.tar.gz
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sha256: {{ sha256 }}
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build:
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number: 0
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run_exports:
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- {{ pin_subpackage(name, max_pin="x") }}
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source:
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url: https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/edirect.tar.gz
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sha256: {{ sha256 }}
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requirements:
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build:
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- {{ compiler('go') }}
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- go-licenses
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run:
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- wget
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@@ -38,7 +39,9 @@ test:
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about:
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home: "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/README"
4041
license: "Public Domain"
41-
summary: "Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process."
42+
summary: "Entrez Direct (EDirect) - Access to NCBI's Entrez databases"
43+
description: |
44+
Entrez Direct (EDirect) provides access to Entrez, the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats.
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doc_url: "https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/{{ version }}.{{ date }}/README"
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extra:
@@ -47,3 +50,5 @@ extra:
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- osx-arm64
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identifiers:
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- biotools:entrez
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skip-lints:
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- compiler_needs_stdlib_c

‎recipes/gffread/meta.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -1,20 +1,20 @@
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{% set name = "gffread" %}
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{% set version = "0.12.7" %}
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{% set version = "0.12.9" %}
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://github.com/gpertea/gffread/releases/download/v{{ version }}/gffread-{{ version }}.tar.gz
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sha256: bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5
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sha256: 3ee1a3a2db938569bcccb1e8d908503392ebf0a3f203ddaff1b967b8ade614d1
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patches:
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- Makefile.patch
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build:
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number: 6
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number: 0
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run_exports:
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- {{ pin_subpackage("gffread", max_pin="x.x") }}
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- {{ pin_subpackage(name, max_pin="x.x") }}
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requirements:
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build:
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- biotools:gffread
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- usegalaxy-eu:gffread
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- doi:10.12688/f1000research.23297.2
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skip-lints:
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- compiler_needs_stdlib_c

‎recipes/htseq/meta.yaml‎

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sha256: {{ sha256 }}
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build:
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number: 0
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number: 2
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script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
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run_exports:
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- {{ pin_subpackage('htseq', max_pin="x") }}
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- {{ pin_subpackage(name, max_pin="x") }}
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requirements:
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build:
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- {{ compiler('cxx') }}
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host:
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- python >=3.10
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- python
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- pip
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- cython
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- setuptools >=74.1
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- numpy
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- pysam >=0.15.1
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- pysam
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- swig >=3.0.8
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run:
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- python >=3.10
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- {{ pin_compatible('numpy') }}
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- matplotlib-base >=1.4
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- python
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- matplotlib-base
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- numpy
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- pysam >=0.15.1
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- scipy >=1.5.0
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- pandas >=1.1.0
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- pysam
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- scipy
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- anndata
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- loompy
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test:
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imports:
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- biotools:htseq
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- usegalaxy-eu:htseq_count
7373
- doi:10.1093/bioinformatics/btu638
74+
- doi:10.1093/bioinformatics/btac166
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skip-lints:
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- compiler_needs_stdlib_c

‎recipes/savvy/meta.yaml‎

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{% set name = "savvy" %}
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{% set version = "2.1.0" %}
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{% set version = "2.2.0" %}
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package:
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name: {{ name|lower }}
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name: {{ name }}
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version: {{ version }}
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source:
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url: https://github.com/statgen/savvy/archive/v{{ version }}.tar.gz
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sha256: 83ebd88c097799b3bbf771dc8ebf6892797ca7a1f49c2d1665d52cfc1bf9e1de
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sha256: f96585faddeba9dd6bbf22f828ecb9f866cc7075947dd25f89c1a618cb9f3bb5
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patches:
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# Fixing postrelease issues
1313
- patches/0002-patch-cmakelists-for-conda-build.patch
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build:
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number: 0
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skip: True # [win]
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number: 4
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run_exports:
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- {{ pin_subpackage(name, max_pin = "x") }}
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- {{ pin_subpackage(name, max_pin="x") }}
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requirements:
2322
build:
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- make
2523
- {{ compiler('c') }}
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- {{ compiler('cxx') }}
25+
- pkg-config
2726
- cmake <4
2827
- make # [not win]
2928
host:
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4140
- sav --help
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4342
about:
44-
home: https://github.com/statgen/savvy
45-
license: MPL-2.0
43+
home: "https://github.com/statgen/savvy"
44+
license: "MPL-2.0"
4645
license_family: MOZILLA
4746
license_file: LICENSE
4847
summary: 'Interface to various variant calling formats.'
49-
dev_url: https://github.com/statgen/savvy
48+
dev_url: "https://github.com/statgen/savvy"
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extra:
5251
additional-platforms:
5352
- linux-aarch64
54-
53+
- osx-arm64
5554
recipe-maintainers:
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- matuskosut
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- jonathonl
57+
skip-lints:
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- compiler_needs_stdlib_c

‎recipes/vafator/meta.yaml‎

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Original file line numberDiff line numberDiff line change
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{% set name = "vafator" %}
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{% set version = "2.2.2" %}
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{% set version = "3.0.0" %}
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package:
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name: "{{ name|lower }}"
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version: "{{ version }}"
5+
name: {{ name }}
6+
version: {{ version }}
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source:
9-
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
10-
sha256: 2390443d1e51466c159abd8b7c58de1b13170a4ce90ea252dc6164c33215b34f
9+
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
10+
sha256: aacc929d8c995a34dd6195e29355cd6f1fa90903e877fcf2f1a09d64e4a4e325
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build:
1313
number: 0
1414
noarch: python
1515
entry_points:
16-
- vafator=vafator.command_line:annotator
17-
- multiallelics-filter=vafator.command_line:multiallelics_filter
18-
- vafator2decifer=vafator.command_line:vafator2decifer
19-
- hatchet2bed=vafator.command_line:hatchet2bed
20-
script: "{{ PYTHON }} -m pip install . -vv"
16+
- vafator = vafator.command_line:annotator
17+
- multiallelics-filter = vafator.command_line:multiallelics_filter
18+
- vafator2decifer = vafator.command_line:vafator2decifer
19+
- hatchet2bed = vafator.command_line:hatchet2bed
20+
script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
2121
run_exports:
22-
- {{ pin_subpackage('vafator', max_pin="x") }}
22+
- {{ pin_subpackage(name, max_pin="x") }}
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requirements:
2525
host:
26-
- cyvcf2 >=0.30.14,<0.31
27-
- pandas >=1.3.3,<1.4
26+
- python >=3.11,<3.12
2827
- pip
29-
- pysam >=0.19.1,<0.20
30-
- python >=3.7,<=3.9
31-
- pybedtools >=0.9.0,<0.10
32-
- logzero >=1.7.0,<1.8
33-
- scipy >=1.8.1,<1.9
3428
run:
35-
- cyvcf2 >=0.30.14,<0.31
36-
- pandas >=1.3.3,<1.4
37-
- pysam >=0.19.1,<0.20
38-
- python >=3.7,<=3.9
39-
- pybedtools >=0.9.0,<0.10
40-
- logzero >=1.7.0,<1.8
41-
- scipy >=1.8.1,<1.9
29+
- python >=3.11,<3.12
30+
- pandas >=3.0.1
31+
- pysam >=0.21.0
32+
- cyvcf2 >=0.31,<0.32
33+
- logzero >=1.7.0,<2
34+
- pybedtools >=0.12.0,<0.13
35+
- numpy >=2.4.3
36+
- scipy >=1.17.1,<2
37+
- setuptools
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test:
4440
imports:
@@ -59,7 +55,7 @@ about:
5955
alignment files. We implement a set of basic coverage annotations and also more sophisticated published
6056
annotations used to assess the quality of every variant call."
6157
doc_url: "https://github.com/tron-bioinformatics/vafator"
62-
dev_url:
58+
dev_url: "https://github.com/tron-bioinformatics/vafator"
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extra:
6561
recipe-maintainers:

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