Merge branch 'master' into bulk

bioconda · Jan 11, 2024 · c0b235d · c0b235d
2 parents 7087233 + 4611e36
commit c0b235d
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diff --git a/recipes/aci/meta.yaml b/recipes/aci/meta.yaml
@@ -0,0 +1,49 @@
+{% set name = "aci" %}
+{% set repo = "amplicon_coverage_inspector" %}
+{% set version = "1.2.20231229" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.io/packages/source/{{ repo[0] }}/{{ repo }}/{{ repo }}-{{ version }}.tar.gz
+  sha256: f54b1829a8eb1972751fce0b5d6a7d48a62d9cc80935a609302779a9966f104d
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - aci=aci.aci:main
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  run_exports:
+    - {{ pin_subpackage('aci', max_pin='x') }}
+
+requirements:
+  host:
+    - python >=3.7,<4.0
+    - pip
+  run:
+    - python >=3.7,<4.0
+    - matplotlib-base >=3.8.2
+    - numpy >=1.26.2
+    - pandas >=2.1.4
+    - pysam >=0.22.0
+
+test:
+  imports:
+    - aci
+  commands:
+    - aci --help
+
+about:
+  home: https://github.com/erinyoung/ACI
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: Visualizes coverage for amplicons
+  doc_url: https://github.com/erinyoung/ACI/blob/main/README.md
+
+extra:
+  recipe-maintainers:
+    - erinyoung
diff --git a/recipes/adam/meta.yaml b/recipes/adam/meta.yaml
@@ -1,19 +1,21 @@
-{% set version="1.0" %}
+{% set version="1.0.1" %}
 
 package:
   name: adam
   version: {{ version }}
 
 source:
   url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/adam/adam-distribution-spark3_2.12/{{ version }}/adam-distribution-spark3_2.12-{{ version }}-bin.tar.gz
-  sha256: 1c1d91ccb42d2faaefb075f93a11bfb5a8c6dd575c7f01d21842a8957204f705
+  sha256: cd6259148a2d9d8bf10549cedd09fe5b12d9f34a25e80a4025f96d60e50be807
   patches:
     - adam-shell.patch
     - adam-submit.patch
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('adam', max_pin="1") }}
 
 requirements:
   run:

diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml
@@ -1,7 +1,7 @@
 {% set name="ampliconsuite" %}
-{% set AS_version="1.2.0" %}
+{% set AS_version="1.2.1" %}
 {% set AA_version="1.3.r7" %}
-{% set AC_version="1.1.0" %}
+{% set AC_version="1.1.1" %}
 
 package:
     name: {{ name }}
@@ -11,12 +11,12 @@ source:
     # the sha256 sum is generated by doing
     # $ wget -O- [URL] | shasum -a 256
     - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz
-      sha256: 749aa74579aa19d400078fc045d1f1d943159b2ebdcd43a449ee7d5ab2d8ca6d
+      sha256: 79515b2c1a57a8ea22905737f3c02047a4319d7ab91554dff1a058ead653c720
     - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz
       sha256: be65a0293da9ced3f6f744657db475c16dd4dcaf9f037e17ee1a19f4ceaa7430
       folder: ampliconarchitectlib
     - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz
-      sha256: e656b557fd8e1c598dd8df9b29e25d4208cb0e1c66e97235c27104751654b7f6
+      sha256: 040400d2eb0b4c847245666a481de927eb0c9a368088c1e97f117e7a228c8c5d
 
 build:
     noarch: python

diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.32.0" %}
+{% set version = "0.33.0" %}
 
 package:
   name: annonars
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/bihealth/annonars/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 467ebd15737c4a6451f5993fa1e93f52c5ecb4a1cdf0b0cd754b414261730f37
+  sha256: 258cfc2aee680718fc1acc8bccddb571416e425198ca258ee295cdc42cc19f71
 
 requirements:
   build:

diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml
@@ -0,0 +1,60 @@
+{% set name = "annosine2" %}
+{% set version = "1.0.4" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
+  sha256: c9d12adec9875c4a429c6e9da5b76d31c760ef7474635caf742d25592378f34c
+
+build:
+  number: 1
+  entry_points:
+    - annosine2 = AnnoSINE.AnnoSINE_v2:main
+  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
+  run_exports:
+        - {{ pin_subpackage('annosine2', max_pin="x") }}
+  noarch: python
+
+requirements:
+  host:
+    - pip
+    - python
+  run:
+    - cycler ==0.10.0
+    - kiwisolver
+    - matplotlib-base
+    - numpy
+    - pandas
+    - pillow
+    - pyparsing
+    - python
+    - python-dateutil
+    - six
+    - hmmer ==3.3.1
+    - minimap2 ==2.26
+    - nodejs ==18.12.1
+    - trf ==4.09
+    - irf ==3.08
+    - cd-hit ==4.8.1
+    - repeatmasker ==4.1.2.p1
+    - seqtk ==1.4
+
+
+test:
+  imports:
+    - AnnoSINE
+  commands:
+    - annosine2 --help
+
+about:
+  home: https://github.com/liaoherui/AnnoSINE
+  license: MIT
+  license_family: MIT
+  summary: AnnoSINE2 - SINE Annotation Tool for Plant and Animal Genomes
+
+extra:
+  recipe-maintainers:
+    - liaoherui
diff --git a/recipes/antismash-lite/build.sh b/recipes/antismash-lite/build.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
 
 echo "include antismash/detection/genefinding/data/train_crypto" >> MANIFEST.in
-df -h 
-$PYTHON -m pip install . --ignore-installed --no-deps -vv
+df -h
+$PYTHON -m pip install . --no-build-isolation --no-deps --no-cache-dir -vvv
diff --git a/recipes/antismash-lite/meta.yaml b/recipes/antismash-lite/meta.yaml
@@ -1,59 +1,65 @@
-{% set name = "antiSMASH-lite" %}
-{% set version = "6.1.1" %}
-{% set sha256 = "38c9fa8d34dea2552d3b21e3cb2ca293864f2f53d381764de9dd3d5f0b40139e" %}
+{% set name = "antismash-lite" %}
+{% set version = "7.1.0" %}
+{% set sha256 = "5c01cce48ef5cc2bc60bfd2e185a5937e731e86a711c4c822a336640984e9b48" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
-build:
-  number: 1
-  noarch: python
-
 source:
   url: https://dl.secondarymetabolites.org/releases/{{ version }}/antismash-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - download-antismash-databases=antismash.download_databases:_main
+    - antismash=antismash.__main__:entrypoint
+  run_exports:
+    - {{ pin_subpackage('antismash-lite', max_pin="x") }}
+
 requirements:
   host:
-    - python >=3.7
+    - python >=3.9
     - pip
   run:
-    - python >=3.7
+    - python >=3.9
+    - brawn >=1.0.1
     - numpy
-    - biopython 1.78
-    - helperlibs >=0.2.0
+    - biopython 1.78.*
+    - helperlibs >=0.2.1
     - jinja2
     - joblib
     - jsonschema
-    - markupsafe >=2.0
+    - markupsafe >=2.1.0
+    - nrpys >=0.1.1
     - pysvg-py3
     - bcbio-gff
-    - pyscss
+    - libsass
     - matplotlib-base
     - scipy
-    - openjdk
-    - scikit-learn >=0.19
-    - diamond >=0.9,<=2.0.15
+    - scikit-learn >=1.3.2
+    - moods >=1.9.4
+    - diamond
     - fasttree 2.1.*
-    - glimmerhmm ==3.0.*
+    - glimmerhmm 3.0.*
     - hmmer2
     - hmmer >=3.1b2
-    - meme <=4.11.2
-    - muscle 3.8.*
+    - meme 4.11.2
     - blast
     - prodigal
 
 test:
+  imports:
+    - antismash
   commands:
-    - antismash -h
-    - blastp -help
-    - fasttree -help
-    - diamond --help 2>&1 > /dev/null
+    - antismash --help
+    - download-antismash-databases --help
 
 about:
   home: https://docs.antismash.secondarymetabolites.org/intro/
-  license: AGPL-3.0
+  license: AGPL-3.0-or-later
   license_family: AGPL
   license_file: LICENSE.txt
   summary: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
@@ -72,4 +78,5 @@ extra:
     - doi:10.1093/nar/gkx319
     - doi:10.1093/nar/gkz310
     - doi:10.1093/nar/gkab335
+    - doi:10.1093/nar/gkad344
     - usegalaxy-eu:antismash
diff --git a/recipes/assemblycomparator2/meta.yaml b/recipes/assemblycomparator2/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.5.14" %}
+{% set version = "2.5.15" %}
 
 package:
   name: assemblycomparator2
   version: {{ version }}
 
 source:
   url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: d95f39d996330ab72ceffc5e8aa17b9348b39478fd2a4bfd01ca960adff2d20e
+  sha256: 9605f4021710e975365090fba1c13c2005c46978cec48c6cabe678167c86d33e
 
 
 build:
@@ -17,7 +17,7 @@ build:
 
 requirements:
   run:
-    - snakemake >=7.32.3
+    - snakemake =7.32.4
     - mamba >=1.4.9 # Necessary for snakemake to install child environments during development.
 
 

diff --git a/recipes/bioframe/meta.yaml b/recipes/bioframe/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bioframe" %}
-{% set version = "0.5.1" %}
+{% set version = "0.6.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 416132f14334f3921d700a692bf94ea21161ca608e5e3b9a119f97c01012d578
+  sha256: 63aec69ac37aebcdc8298ed41154a875ba99652cc7ef081dd1458bc90537f73b
 
 build:
   noarch: python

diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml
@@ -1,15 +1,17 @@
-{% set version = "0.38.1" %}
+{% set version = "0.38.2" %}
 
 package:
   name: breseq
   version: '{{ version }}'
 
 source:
   url: https://github.com/barricklab/breseq/releases/download/v{{ version }}/breseq-{{ version }}-Source.tar.gz
-  sha256: "92af34f7248f7c8cf65951e1b86ffc0d6f7446dbe9d3323aa43c577ea1ff48b3"
+  sha256: "d451670b9e7e3c87b76d3107efe7f1a9a94904011a32e5d407f4cce7ee3b2892"
 
 build:
-  number: 1
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('breseq', max_pin="x.x") }}
 
 requirements:
   build:
@@ -31,8 +33,9 @@ test:
 
 about:
   home: https://github.com/barricklab/breseq
-  license: GPL-3.0
+  license: GPL-2.0-or-later
   license_family: GPL
   license_file: COPYING
   summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
     data.
+  doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/"
diff --git a/recipes/bustools/meta.yaml b/recipes/bustools/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "0.43.1" %}
+{% set version = "0.43.2" %}
 
 package:
   name: bustools
   version: {{ version }}
 
 source:
   url: https://github.com/BUStools/bustools/archive/v{{ version }}.tar.gz
-  sha256: ac94a33ca459de81c5756825a7a7f8daeae357fc6bf0ef88d4900e77b70f2b90
+  sha256: ad5816152644ee615316daecf5883183994bd7cc96e6c008439123f4cd750b1f
 
 build:
   number: 0

diff --git a/recipes/cannoli/meta.yaml b/recipes/cannoli/meta.yaml
@@ -1,16 +1,18 @@
-{% set version="1.0" %}
+{% set version="1.0.1" %}
 
 package:
   name: cannoli
   version: {{ version }}
 
 source:
   url: https://search.maven.org/remotecontent?filepath=org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/{{ version }}/cannoli-distribution-spark3_2.12-{{ version }}-bin.tar.gz
-  sha256: 28c076ebd64278c07e9169e5b5de13ea5fd30a1f68daffbe551518092089ef6a
+  sha256: 4cfbbe1d2085298e62d4143116f8776ef2c91854f36a0803c27164c51b541e12
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('cannoli', max_pin="1") }}
 
 requirements:
   run: