Merge branch 'master' into update_my_recipe

bioconda · Nov 24, 2024 · 3598d52 · 3598d52
2 parents ade06ba + 29c9e9f
commit 3598d52
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diff --git a/recipes/agc/meta.yaml b/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

diff --git a/recipes/ampcombi/meta.yaml b/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:

diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "artic" %}
-{% set version = "1.5.3" %}
-{% set sha256 = "107483f22de571c4aafae91c475e453d939e6a8e85a7e2cd2d23ccbca224ef1c" %}
+{% set version = "1.5.5" %}
+{% set sha256 = "bf792741239a04a285e6f972a064fc32b3d542db5eeb6c0d169055f94fef2cfb" %}
 
 package:
   name: {{ name|lower }}
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: python
   run_exports:
     - {{ pin_subpackage('artic', max_pin='x.x') }}
@@ -43,12 +43,11 @@ requirements:
     - htslib
     - minimap2
     - multiqc
-    - muscle <5.1
+    - mafft
     - pandas
     - pysam
     - pytest 
     - cyvcf2
-    - pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE
     - requests
     - samtools
     - tqdm

diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "26.1.0" %}
+{% set version = "26.2.0" %}
 
 package:
   name: augur
   version: {{ version }}
 
 source:
   url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
-  sha256: 74159e9a663ad4f1171b1800dd345dd94777a37dcc74abc754351626f75668c2
+  sha256: a501c10b0242384d33f5fd02ab943d4b295e80f31e2a14b6a9692f01e17ac5af
 
 build:
   number: 0
@@ -33,7 +33,7 @@ requirements:
     - networkx >=2.5,<4
     - numpy >=1.0.0,<2
     - packaging >=19.2
-    - pandas >=1.0.0,<2
+    - pandas >=1.0.0,<3
     - pyfastx >=1.0.0,<3
     - python-calamine >=0.2.0
     - scipy >=1.0.0,<2

diff --git a/recipes/aviary/meta.yaml b/recipes/aviary/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.9.2" %}
+{% set version = "0.10.0" %}
 {% set name = "aviary" %}
-{% set sha256 = "83e18bbd2abf347ae7e0d83d81d671031a6a98324b01053e79c0d86b989c95ba" %}
+{% set sha256 = "a7ff834830fcfa7c4754a3881530875d9a1210d4c532be6a8391b9747645742e" %}
 
 package:
   name: aviary

diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "BBMap" %}
-{% set version = "39.11" %}
-{% set sha256 = "bcb80b109757a638d6c767b7ba785fde5111437f7025e0a93dce587cdfaa2795" %}
+{% set version = "39.13" %}
+{% set sha256 = "6920a94549d3fca129e031cc14e5306ae571a223410e1f116b0292e530c433de" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/bed2gtf/meta.yaml b/recipes/bed2gtf/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bed2gtf" %}
-{% set version = "1.9.2" %}
+{% set version = "1.9.3" %}
 
 package:
  name: {{ name }}
  version: {{ version }}
 
 source:
  url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz
- sha256: 38bd7528a5a643a4ade316838af36085809bf6476d1b8f37f126d7678fb7e15f
+ sha256: c6a0b2ea31719932ef6cf002e68d72579daaa327d993da0069b302b51b1b7439
 
 build:
  number: 0

diff --git a/recipes/biobb_godmd/meta.yaml b/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

diff --git a/recipes/biobb_gromacs/meta.yaml b/recipes/biobb_gromacs/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_gromacs" %}
-{% 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: dc57bbba78f24fedc9931197fb321428d27078b56b41dd1aafd822c68387cb73
+  sha256: 73c158f537c172c8325d7b6db8748761addf89bf08213aefef66b2a6bd671a3d
 
 build:
   number: 0
@@ -18,13 +18,13 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - gromacs ==2022.2
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - gromacs ==2022.2
 
 test:

diff --git a/recipes/biobb_haddock/meta.yaml b/recipes/biobb_haddock/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_haddock" %}
-{% set version = "4.2.1" %}
+{% 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: cfd558d0683b3ac9f517aef5c68a801c34efe3d1b6ab948c1a44c3976be5b105
+  sha256: 6a41e63280f577e16e923bc1027967c37a3dfca823cc21803324c6fe33786bb8
 
 build:
   number: 0
@@ -20,10 +20,10 @@ requirements:
   host:
     - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
   run:
     - python >=3.9
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
 
 test:
   imports:

diff --git a/recipes/biobb_io/meta.yaml b/recipes/biobb_io/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_io" %}
-{% 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: e20b38cb73e956eccd0ff61fef5212da2e52cb7c625664794a50f24b7cfbecd3
+  sha256: bcc7edea8abb40e0332ff069931e4db1a9ad6af3cae1a8b09af29d3a6d1572d7
 
 build:
   number: 0
@@ -18,12 +18,12 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
 test:
   imports:
     - biobb_io

diff --git a/recipes/biobb_mem/meta.yaml b/recipes/biobb_mem/meta.yaml
@@ -1,24 +1,26 @@
 {% set name = "biobb_mem" %}
-{% set version = "5.0.1" %}
+{% 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: bb82d828a3be20ca577162aca4ae9a7073598a08f181e079277c7f13f1e1950c
+  sha256: f307bb5f51e7ae5802401eabd24ed2d35e405e4d0b09847b9f2a58aa53a77308
 
 build:
-  number: 0
+  number: 1
   noarch: python
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
+  script: 
+    - "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   host:
     - python >=3.9
+    - pip
     - setuptools
     - biobb_common ==5.0.0
     - lipyphilic ==0.10.0
@@ -27,23 +29,28 @@ requirements:
     - hole2
   run:
     - python >=3.9
+    - pip
     - biobb_common ==5.0.0
     - lipyphilic ==0.10.0
     - ambertools >=22.5
     - gromacs
     - hole2
+  commands:
+    - pip install fatslim --no-deps
+
 test:
   imports:
     - biobb_mem
-    - biobb_mem.mdanalysis_biobb
-    - biobb_mem.lipyphilic_biobb
     - biobb_mem.ambertools
+    - biobb_mem.fatslim
+    - biobb_mem.lipyphilic_biobb
+    - biobb_mem.mdanalysis_biobb
 
 about:
   home: https://github.com/bioexcel/biobb_mem
   license: Apache Software License
   license_family: APACHE
-  license_file: ''
+  license_file: LICENSE
   summary: Biobb_mem is the Biobb module for membrane structure analysis.
   description: "# biobb_mem\n\n### Introduction\nBiobb_mem is the Biobb module for membrane structure analysis.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\
     \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/).\n\
@@ -53,8 +60,9 @@ about:
     [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\
     \n\
     ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png \"Bioexcel\")\n\n\n"
-  doc_url: ''
-  dev_url: ''
+  doc_url: 'http://biobb-mem.readthedocs.io/en/latest/'
+  dev_url: 'https://github.com/bioexcel/biobb_mem'
 
 extra:
-  recipe-maintainers: ''
+  recipe-maintainers:
+    - RubenChM
diff --git a/recipes/biobb_model/meta.yaml b/recipes/biobb_model/meta.yaml
@@ -1,8 +1,8 @@
 {% set name = "biobb_model" %}
-{% set version = "4.2.3" %}
+{% set version = "5.0.0" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "8c4b87ef92331d060700e5b346cddb718b1cc27b79752b1c8ef3583e0dce0927" %}
+{% set hash_value = "6f0cf1302d1b39404a65199e6aa5b9e4435099c2cef7d948253d20837d03d415" %}
 
 package:
   name: '{{ name|lower }}'
@@ -21,15 +21,15 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
-    - biobb_structure_checking >=3.13.4
+    - biobb_common ==5.0.0
+    - biobb_structure_checking >=3.13.5
     - xmltodict
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
-    - biobb_structure_checking >=3.13.4
+    - python >=3.9
+    - biobb_common ==5.0.0
+    - biobb_structure_checking >=3.13.5
     - xmltodict
 test:
   imports:

diff --git a/recipes/biobb_pdb_tools/meta.yaml b/recipes/biobb_pdb_tools/meta.yaml
@@ -1,30 +1,30 @@
 {% set name = "biobb_pdb_tools" %}
-{% 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: 025d968ba5a5cee692f03d756f0fc474d7dcdec10e2babf150ad10af205aae25
+  sha256: 46cf4312ab7da0bf9491b1bf89677daf6f1163a3163c41d111863cf1baa1bd9a
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - pdb-tools
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - pdb-tools
 test:
   imports: