Merge branch 'master' into neptune

recipes/agc/meta.yaml

@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 1
+  number: 2
   script: "mkdir -p ${PREFIX}/bin; cp agc ${PREFIX}/bin"
   run_exports:
     - {{ pin_subpackage('agc', max_pin="x") }}
@@ -31,6 +31,7 @@ test:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
   skip-lints:
     - should_be_noarch_generic
     - should_not_be_noarch_source

recipes/ampcombi/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "AMPcombi" %}
-{% set version = "0.2.2" %}
+{% set version = "2.0.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: da9a179851a8f2041d05ccd10dd45b58099e84059e2e66a9ee405d1913471b58
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ampcombi-{{ version }}.tar.gz
+  sha256: 4bef05aa8433d991b76b81cb2338396c064f2ace5c73642411b2a2467524a0eb
 
 build:
   noarch: python
@@ -32,9 +32,10 @@ requirements:
     - backports.tempfile
     - contextlib2
     - openpyxl
+    - numpy ==1.26.4
     - jsonschema
     - python ==3.11
-    - diamond ==2.0.15
+    - colorama ==0.4.6
     - mmseqs2 ==15.6f452
 
 test:

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

recipes/bakta/meta.yaml

@@ -1,17 +1,17 @@
-{% set version = "1.10.0" %}
+{% set version = "1.10.1" %}
 
 package:
   name: bakta
   version: '{{ version }}'
 
 source:
   url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
-  sha256: '78f98ead47b45ad5fe66a41be369be72cac36dff6d68073d285c568dc860be98'
+  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
@@ -23,10 +23,10 @@ build:
 
 requirements:
   host:
-    - python >=3.9, <3.12
+    - python >=3.9,<3.12
     - pip
   run:
-    - python >=3.9, <3.12
+    - python >=3.9,<3.12
     - biopython >=1.78
     - xopen >=1.5.0
     - requests >=2.25.1
@@ -58,8 +58,8 @@ test:
 
 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

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

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

recipes/biobb_godmd/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_godmd" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: f697f96f216ce439e058d46842a2507ada30221d7048628fb83676ebf5806c50
+  sha256: edb62b0ca1dc5b8ee89f33cd44e8d2aa6e53ba6fd378f6c193aa6adf603fc282
 
 build:
   number: 0

recipes/breakfast/meta.yaml

@@ -1,49 +1,50 @@
 {% set name = "breakfast" %}
-{% set version = "0.4.3" %}
+{% set version = "0.4.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/breakfast-{{ version }}.tar.gz
-  sha256: a241e0d4891c62635f1b99559271fb4b7777ffa60ef67e25be579d6750c01b9c
+  sha256: 5dd370d4d6d92d7b161acc5356b3b6c7f454d9c0665a8abac38e5f6c012d3eee
 
 build:
   entry_points:
     - breakfast = breakfast.console:main
+  run_exports:
+    - {{ pin_subpackage('breakfast', max_pin="x.x") }}
   noarch: python
-  script: {{ PYTHON }} -m pip install . -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
   number: 0
 
 requirements:
   host:
     - pip
-    - poetry
-    - python >=3.6,<3.11
+    - poetry-core
+    - python >=3.11,<3.13
   run:
-    - click >=8.1.3,<9.0.0
-    - networkx >=2.8,<3.0
-    - numpy >=1.22.3,<2.0.0
-    - pandas >=1.4.2,<2.0.0
+    - click >=8.1.7,<9.0.0
+    - networkx >=3.4.2,<4.0.0
+    - numpy >=2.1.3,<3.0.0
+    - pandas >=2.2.3,<3.0.0
     - python >=3.9,<3.11
-    - scikit-learn >=1.0.2,<2.0.0
-    - scipy >=1.8.0,<2.0.0
+    - scikit-learn >=1.5.2,<2.0.0
+    - scipy >=1.14.1,<2.0.0
 
 test:
   imports:
     - breakfast
   commands:
-    - pip check
     - breakfast --help
-  requires:
-    - pip
 
 about:
   home: https://github.com/rki-mf1/breakfast
-  summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs'
+  summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs.'
   license: MIT
+  license_family: MIT
   license_file: LICENSE
+  dev_url: https://github.com/rki-mf1/breakfast
 
 extra:
   recipe-maintainers:

recipes/cnvkit/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "cnvkit" %}
-{% set version = "0.9.11" %}
+{% set version = "0.9.12" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz
-  sha256: 1763936427184270108fd51219ebc82f542e28339bdec587579b8745f61179a8
+  sha256: 39d65ba3d9c541dfd80986ace298b2d521067d1b81edef7169196b8dcc5d63d5
 
 build:
   noarch: python
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - bioconductor-dnacopy
@@ -49,13 +50,13 @@ test:
     - cnvkit.py -h
 
 about:
-  home: https://github.com/etal/cnvkit
-  license: Apache-2.0
+  home: "https://github.com/etal/cnvkit"
+  license: "Apache-2.0"
   license_family: APACHE
   license_file: LICENSE
-  summary: Copy number variant detection from high-throughput sequencing
-  dev_url: https://github.com/etal/cnvkit
-  doc_url: https://cnvkit.readthedocs.io/en/stable/
+  summary: "Copy number variant detection from high-throughput sequencing."
+  dev_url: "https://github.com/etal/cnvkit"
+  doc_url: "https://cnvkit.readthedocs.io/en/stable"
 
 extra:
   identifiers:

recipes/ebi-eva-common-pyutils/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "ebi-eva-common-pyutils" %}
-{% set version = "0.6.10" %}
+{% set version = "0.6.11" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz
-  sha256: f143c703e31f40c94ebe366ba5f8a8247b6c825590ac157a7f5495f36aa7accb
+  sha256: 503f15c55b8438295727661486d610e87b7e9c9ca159ff8e373d0533094eb93b
 
 build:
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation

recipes/gfainject/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "gfainject" %}
-{% set version = "0.1.0" %}
+{% set version = "0.1.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/AndreaGuarracino/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: a4388e524d5942f53d2fa94a93b2e82c926506c27cfdf04c04fbe8669a7ecebf 
+  sha256: a11f41ee94614d8c089454fdb3d0fb96e2f305db46895e2f64d974fa1707e739 
 
 build:
   number: 0
@@ -17,6 +17,11 @@ build:
 requirements:
   build:
     - {{ compiler('rust') }}
+    - cmake
+    - make
+    - pkg-config
+    - {{ compiler('c') }}      # For zlib-ng compilation
+    - {{ compiler('cxx') }}    # For C++ dependencies if any
 
 test:
   commands:

recipes/gubbins/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "gubbins" %}
-{% set version = "3.3.5" %}
-{% set sha256 = "4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774" %}
+{% set version = "3.4" %}
+{% set sha256 = "ff134b7c1d06eee548e94f417394fb67229caf1b0d35b097a71309017ac7a91d" %}
 
 package:
   name: {{ name|lower }}
@@ -29,6 +29,7 @@ requirements:
     - perl
     - zlib
     - python >=3.8,<3.10
+    - pip
     - scipy
     - setuptools
     - dendropy

recipes/harpy/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "1.11" %}
-{% set sha256 = "e48308505e8ef9e6be2fdce8cb449f9fffe1aabcf1fb6b6e2aba94a8b00ccc71" %}
+{% set version = "1.12" %}
+{% set sha256 = "e6b0ecdd862d154b8c5de6c1414a131e0b5d2f8449edbe85425f9bc9534525db" %}
 
 package:
   name: harpy

recipes/hmftools-redux/meta.yaml

@@ -12,13 +12,13 @@ source:
 
 build:
   noarch: generic
-  number: 5
+  number: 6
   run_exports:
     - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}
 
 requirements:
   run:
-    - openjdk >=8
+    - openjdk >=8,<=21
     - sambamba >=1.0.1
 
 test: