Merge branch 'bioconda:master' into master

bioconda · Nov 19, 2024 · bf23465 · bf23465
2 parents 3755411 + ebcf6a3
commit bf23465
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diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "argo" %}
-{% set version = "0.1.2" %}
+{% set version = "0.1.3" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0
+  sha256: c6be3e1efc744a591524979a53895f9cbd70962a1825d8e2b442f5ffb7a3cc6b
 
 build:
   noarch: python

diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml
@@ -1,83 +1,76 @@
 {% set name = "artic" %}
-{% set version = "1.2.4" %}
-{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %}
+{% set version = "1.5.3" %}
+{% set sha256 = "107483f22de571c4aafae91c475e453d939e6a8e85a7e2cd2d23ccbca224ef1c" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version|replace("-", "_") }}
+
 source:
   url: https://github.com/artic-network/fieldbioinformatics/archive/v{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   noarch: python
   run_exports:
     - {{ pin_subpackage('artic', max_pin='x.x') }}
-  script: python -m pip install --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   entry_points:
     - artic=artic.pipeline:main
     - align_trim=artic.align_trim:main
-    - align_trim_n=artic.align_trim_n:main
     - margin_cons=artic.margin_cons:main
-    - margin_cons_medaka=artic.margin_cons_medaka:main
     - vcfextract=artic.vcfextract:main
     - artic_vcf_merge=artic.vcf_merge:main
     - artic_vcf_filter=artic.vcf_filter:main
     - artic_make_depth_mask=artic.make_depth_mask:main
     - artic_fasta_header=artic.fasta_header:main
     - artic_mask=artic.mask:main
-    - artic_get_stats=artic.artic_mqc:main
+    - artic_get_models=artic.get_models:main
 
 requirements:
   host:
-    - python >=3
+    - python ==3.9
     - pip
+    - setuptools
   run:
-    - python
-    - artic-porechop >=0.3.2pre
-    - artic-tools
-    - longshot
+    - python ==3.9
     - bcftools
     - biopython
     - bwa
+    - clair3
     - clint
     - htslib
-    - medaka >=1.10.0
-    - minimap2 >=2.26
+    - minimap2
     - multiqc
-    - muscle =3.8
-    - nanopolish >=0.14.0
+    - muscle <5.1
     - pandas
-    - pip
     - pysam
     - pytest 
-    - pyvcf
+    - cyvcf2
     - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE
     - requests
     - samtools
     - tqdm
-    - keras-preprocessing >=1.1.2
-
 
 test:
   commands:
     - artic -h
     - align_trim -h
-    - align_trim_n -h
     - margin_cons -h
-    - margin_cons_medaka -h
     - vcfextract -h
     - artic_vcf_merge -h
     - artic_vcf_filter -h
     - artic_make_depth_mask -h
     - artic_fasta_header -h
     - artic_mask -h
-    - artic_get_stats -h
+    - artic_get_models -h
 
 about:
     home: https://github.com/artic-network/fieldbioinformatics
     license: MIT
+    license_family: MIT
     license_file: LICENSE
-    summary: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
-
+    summary: "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore."
+    dev_url: https://github.com/artic-network/fieldbioinformatics
+    doc_url: https://artic.readthedocs.io/en/latest
diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.7.4" %}
+{% set version = "3.0.0" %}
 
 package:
   name: arvados-python-client
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz
-  sha256: 932398da39daba88041f1084d19019e7300cac462ef93f181f40aa85562ff275
+  sha256: 7f980029b27a27f0f348f610784757ca6ff419aee6eb903b046c37b719e1b820
 
 build:
   noarch: python
@@ -35,6 +35,7 @@ requirements:
     - protobuf <4.0.0
     - pyparsing <3
     - dataclasses
+    - websockets
 
 test:
   imports:

diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml
@@ -1,26 +1,27 @@
-{% set version = "26.0.0" %}
+{% set version = "26.1.0" %}
 
 package:
   name: augur
   version: {{ version }}
 
 source:
   url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
-  sha256: 0040d881eca4d695b75ba87c07a6c7abbdd13cc3e200606d77b38b875348cb07
+  sha256: 74159e9a663ad4f1171b1800dd345dd94777a37dcc74abc754351626f75668c2
 
 build:
   number: 0
   noarch: python
   entry_points:
     - augur = augur.__main__: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"
   run_exports:
     - {{ pin_subpackage('augur', max_pin='x') }}
 
 requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - bcbio-gff >=0.7.1,<0.8
@@ -38,7 +39,6 @@ requirements:
     - scipy >=1.0.0,<2
     - treetime >=0.11.2,<0.12
     - xopen[zstd] >=1.7.0,<3
-
     - fasttree
     - iqtree
     - mafft
@@ -52,15 +52,18 @@ test:
     - augur --help
 
 about:
-  home: https://github.com/nextstrain/augur
-  license: AGPL-3.0-only
-  summary: 'Process pathogen genome data for the Nextstrain platform'
+  home: "https://github.com/nextstrain/augur"
+  license: "AGPL-3.0-only"
+  summary: 'Process pathogen genome data for the Nextstrain platform.'
   license_family: AGPL
   license_file: LICENSE.txt
+  dev_url: "https://github.com/nextstrain/augur"
+  doc_url: "https://docs.nextstrain.org/projects/augur"
 
 extra:
   identifiers:
     - doi:10.21105/joss.02906
+    - biotools:Augur
   recipe-maintainers:
     - nextstrain-bot
     - huddlej

diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml
@@ -1,61 +1,65 @@
-{% set version = "1.9.4" %}
+{% set version = "1.10.1" %}
 
 package:
   name: bakta
   version: '{{ version }}'
 
 source:
   url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
-  sha256: 'ad92853e9d4f022024d393149eb086ad36a7e35f824a5d9efed94c3262f9cf66'
+  sha256: '4a13b7362dd46d44edc175956afda2478122b48bfef4fb9581c198b35fd36296'
 
 build:
   noarch: python
   number: 0
-  script: python -m pip install --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
   entry_points:
     - bakta = bakta.main:main
     - bakta_proteins = bakta.proteins:main
     - bakta_db = bakta.db:main
     - bakta_plot = bakta.plot:main
+    - bakta_io = bakta.json_io:main
   run_exports:
     - {{ pin_subpackage('bakta', max_pin='x.x') }}
 
 requirements:
   host:
-    - python >=3.8, <3.11
+    - python >=3.9,<3.12
     - pip
   run:
-    - python >=3.8, <3.11
+    - python >=3.9,<3.12
     - biopython >=1.78
     - xopen >=1.5.0
     - requests >=2.25.1
     - alive-progress ==3.0.1
     - pyyaml >=6.0
-    - pyrodigal >=3.1.0
+    - pyrodigal >=3.5.0
     - trnascan-se >=2.0.11
     - aragorn >=1.2.41
     - infernal >=1.1.4
     - piler-cr
-    - pyhmmer >=0.10.4
-    - diamond ==2.1.8
+    - pyhmmer >=0.10.15
+    - diamond >=2.1.10
     - blast >=2.14.0
-    - ncbi-amrfinderplus >=3.11.26
-    - circos >=0.69.8
+    - ncbi-amrfinderplus >=4.0.3
+    - pycirclize >=1.7.0
 
 test:
   import:
     - Bio.SeqIO
     - xopen.xopen
-    - pyrodigal
     - requests
     - alive_progress
+    - pyyaml
+    - pyrodigal
+    - pyhmmer
+    - pycirclize
   commands:
     - bakta --help
 
 about:
   home: https://github.com/oschwengers/bakta
-  license: GPLv3
-  license_family: GPL
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
   summary: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
   dev_url: https://github.com/oschwengers/bakta

diff --git a/recipes/beagle/meta.yaml b/recipes/beagle/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "beagle" %}
-{% set version = "5.4_27May24.118" %}
-{% set sha256 = "3b8f0b1dd1f56cccf0dbfd6a53b091829e69e3d693834b814af203be911b0009" %}
+{% set version = "5.4_29Oct24.c8e" %}
+{% set sha256 = "938f0b1ab12385e0686790cef52d7b9491c96c0c1837af5c0d62c9a6576a8956" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://faculty.washington.edu/browning/beagle/beagle.27May24.118.jar
+  url: https://faculty.washington.edu/browning/beagle/beagle.29Oct24.c8e.jar
   sha256: {{ sha256 }}
 
 build:

diff --git a/recipes/biobambam/build.sh b/recipes/biobambam/build.sh
@@ -1,4 +1,9 @@
 #!/bin/bash
 set -eu
-./configure --prefix=${PREFIX}
+
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" \
+	--with-libmaus2 --with-xerces-c --with-gmp \
+	CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 make install
diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "biobambam" %}
-{% set version = "2.0.183" %}
-{% set datestamp = "20210802180148" %}
-{% set sha256hash = "8712ceac509c389111b01dc3429f673dc0f8b77cb2bc48a1ebcf17f6888b2945" %}
+{% set version = "2.0.185" %}
+{% set datestamp = "20221211202123" %}
+{% set sha256 = "e405421e869ac7220c3a7e5da0d24a3c7b4c7b1807e044a439fe68efc88a1f2a" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://gitlab.com/german.tischler/biobambam2/-/archive/{{ version }}-release-{{ datestamp }}/biobambam2-{{ version }}-release-{{ datestamp }}.tar.gz
-  sha256: {{ sha256hash }}
+  sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
@@ -21,19 +21,33 @@ requirements:
   build:
     - make
     - {{ compiler('cxx') }}
+    - autoconf
+    - automake
+    - libtool
+    - pkg-config
   host:
-    - libmaus2 >=2.0.810
+    - libmaus2 >=2.0.813
+    - gmp
+    - xerces-c
+    - zlib
+  run:
+    - libmaus2 >=2.0.813
 
 test:
   commands:
     - bamsormadup --help
     - bamtofastq --help
+
 about:
   home: https://gitlab.com/german.tischler/biobambam2
-  license: GPLv3
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: GPLv3
-  summary: Tools for early stage alignment file processing
+  summary: "Tools for early stage alignment file processing."
+  dev_url: https://gitlab.com/german.tischler/biobambam2
 
 extra:
   additional-platforms:
-    - linux-aarch64
+    - linux-aarch64
+  identifiers:
+    - biotools:biobambam
diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "biobb_chemistry" %}
-{% set version = "5.0.2" %}
+{% set version = "5.0.3" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05
+  sha256: cc89a00439b85b71bd37980cbfe00a2dbbf201613298bac731cd3830c6fb4f6e
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports: