Merge branch 'master' into bulk

bioconda · Dec 29, 2023 · fc39ab3 · fc39ab3
2 parents cef73f3 + 32b8087
commit fc39ab3
Show file tree

Hide file tree

Showing 9 changed files with 37 additions and 57 deletions.
diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.31.2" %}
+{% set version = "0.32.0" %}
 
 package:
   name: annonars
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: c7d953633d77c3c46cf3d9417e9b8e6d67afac2a529dea0e342da3d8bb0d6680
+  sha256: 467ebd15737c4a6451f5993fa1e93f52c5ecb4a1cdf0b0cd754b414261730f37
 
 requirements:
   build:

diff --git a/recipes/chromhmm/meta.yaml b/recipes/chromhmm/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "ChromHMM" %}
-{% set version = "1.24" %}
+{% set version = "1.25" %}
 
 package:
   name: {{ name|lower }}
@@ -8,10 +8,12 @@ package:
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('chromhmm', max_pin=None) }}
 
 source:
   url: https://github.com/jernst98/{{ name }}/archive/v{{ version }}.tar.gz
-  sha256: 84e14ebb78c197abe946007e72965296980339d4e3155604bf6c6734319af30c
+  sha256: 96b5773f7400835f16cc1d86d4e42e6dcc038e74569311cd73da2d5c5002a5d2
 
 requirements:
   run:
@@ -27,6 +29,7 @@ about:
   home: https://github.com/jernst98/ChromHMM
   license: GPLv3
   summary: 'ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.'
+  license_file: LICENSE
 
 extra:
   notes: 'ChromHMM comes with about 36MB of example data which is not included in the recipe. This recipe installs a script, "download_chromhmm_data.sh", which downloads the data in the proper location, and which can be run after ChromHMM has been installed.'

diff --git a/recipes/colabfold/fix-jax-04-nan.patch b/recipes/colabfold/fix-jax-04-nan.patch
diff --git a/recipes/colabfold/meta.yaml b/recipes/colabfold/meta.yaml
@@ -1,7 +1,7 @@
-{% set cf_version = "1.5.3" %}
-{% set cf_hash = "1b2776f285981796559effbc3691ebbcfcde68514cc05559583ebab76c4c25e8" %}
-{% set af_version = "2.3.5" %}
-{% set af_hash = "6244c2143987dd4a6a87c1174c7a801c220034fbeb8d13f901b0f950b69d8543" %}
+{% set cf_version = "1.5.5" %}
+{% set cf_hash = "7fb0ad263c24ec00d46f2dff1611989234bc1351d71653dd06006f2c88f83dcb" %}
+{% set af_version = "2.3.6" %}
+{% set af_hash = "a5674257d92928511d70f94ec3261e275cb3442a7762b5210e01f445692d2182" %}
 
 package:
   name: colabfold
@@ -14,7 +14,7 @@ build:
     python -m pip install --no-deps --ignore-installed alphafold/
   run_exports:
     - {{ pin_subpackage('colabfold', max_pin="x") }}
-  number: 1
+  number: 0
 
 source:
   - url: https://github.com/sokrypton/ColabFold/archive/refs/tags/v{{ cf_version }}.tar.gz
@@ -23,14 +23,12 @@ source:
   - url: https://github.com/steineggerlab/alphafold/archive/refs/tags/v{{ af_version }}.tar.gz
     sha256: {{ af_hash }}
     folder: alphafold
-    patches:
-      - fix-jax-04-nan.patch
 
 requirements:
   host:
     - pip
     - python
-    - poetry
+    - poetry-core >=1.0.0
   run:
     - python
     - absl-py
@@ -42,20 +40,18 @@ requirements:
     - pandas
     - appdirs
     - py3Dmol
-    - dm-haiku
     - dm-tree
     - ml-collections
-    - immutabledict
     - importlib-metadata
-    - biopython
-    - jax ==0.4.14
-    - jaxlib ==0.4.14
-    - chex ==0.1.8
-    - tensorflow ==2.12.1=cpu*
+    - dm-haiku ==0.0.10
+    - biopython <=1.82
+    - jax >=0.4.14
+    - jaxlib >=0.4.14
+    - tensorflow >=2.12.1=cpu*
     - mmseqs2 >=15.6f452
     - kalign2 >=2.04
     - hhsuite >=3.3.0
-    - openmm ==7.7.0
+    - openmm >=7.7.0,<8.1.0
     - pdbfixer
 
 test:

diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml
@@ -1,8 +1,8 @@
 {% set user = "USDA-VS" %}
 {% set name = "GenoFLU" %}
 
-{% set version = "1.01" %}
-{% set sha256 = "c97ad073c2cf14f1c14f1a705ddc3817189c30f03239ba97b068a1ddab90ceb8" %}
+{% set version = "1.02" %}
+{% set sha256 = "8cae43be805ee1822d6acc3d1d51a7c4445c5252b5004ab700b7f807fc78070d" %}
 
 package:
   name: {{ name|lower }}
@@ -11,6 +11,8 @@ package:
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('genoflu', max_pin="x") }}
 
 source:
   url: https://github.com/{{ user }}/{{ name }}/archive/{{ version }}.tar.gz
@@ -30,7 +32,7 @@ test:
 
 about:
   home: https://github.com/{{ user }}/{{ name }}
-  license: GPL3
+  license: GPL-3.0-or-later
   license_file: LICENSE
   summary: Influenza data pipeline to automate genotyping assignment.
-  dev_url: https://github.com/USDA-VS/GenoFLU
+  dev_url: https://github.com/USDA-VS/GenoFLU
diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "LAST" %}
-{% set version = "1521" %}
+{% set version = "1522" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://gitlab.com/mcfrith/last/-/archive/{{ version }}/last-{{ version }}.zip
-  sha256: dcfe5339f048f635f02326d181e086469c16e54a0f674c5df814c4d54236fc26
+  sha256: 0cc27dce53693c4d97864c012f9b9b34e4c02ebd0c38db23c5c5d978dbfd4d4e
 
 build:
   number: 0

diff --git a/recipes/pcaone/meta.yaml b/recipes/pcaone/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.4.0" %}
-{% set sha256 = "b6bf45c20dddcc42811dcc902c7d92c5901d03fb4c69675ee8da39b3c92763a9" %}
+{% set version = "0.4.1" %}
+{% set sha256 = "03f8afa9870507e03aa90a349a00f70f56bbf202b05a4d3d648148f3c30b6518" %}
 
 
 package:

diff --git a/recipes/recognizer/build.sh b/recipes/recognizer/build.sh
diff --git a/recipes/recognizer/meta.yaml b/recipes/recognizer/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "recognizer" %}
-{% set version = "1.9.4" %}
-{% set sha256 = "36c3f08fff9c5eff6bf45491b3332eee44507d08f9839766b4fe81eeb8715630" %}
+{% set version = "1.10.0" %}
+{% set sha256 = "7f001a4fb888777a7b14707f76458f25fc98fe14299d1bdcbf2452eba7cab75f" %}
 
 package:
   name: {{ name|lower }}
@@ -15,6 +15,12 @@ build:
   number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
+  script: >
+    mkdir -p $PREFIX/bin && 
+    mkdir -p $PREFIX/share && 
+    cp recognizer.py resources/*.tsv $PREFIX/share &&
+    chmod +x $PREFIX/share/recognizer.py &&
+    ln -s $PREFIX/share/recognizer.py $PREFIX/bin/recognizer
 
 requirements:
   run: