Merge branch 'master' into saccharis

bioconda · Oct 10, 2024 · df88bf4 · df88bf4
2 parents 56121d0 + 9aec042
commit df88bf4
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diff --git a/.github/workflows/CommentResponder.yml b/.github/workflows/CommentResponder.yml
@@ -1,28 +1,14 @@
 name: CommentResponder
 on:
-  status:
-  # check_suite:
-  #   types:
-  #   - completed
   issue_comment:
     types:
     - created
 
-    # Runs too many times
-    # (
-    #   github.event_name == 'check_suite' &&
-    #   github.event.check_suite.conclusion == 'success'
-    # ) ||
-
 jobs:
   comment:
     runs-on: ubuntu-latest
     name: bioconda-bot comment
     if: >-
-      (
-        github.event_name == 'status' &&
-        github.event.state == 'success'
-      ) ||
       (
         github.event_name == 'issue_comment' &&
         github.event.issue.pull_request &&

diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -179,7 +179,6 @@ recipes/gemma
 recipes/roary
 recipes/deltabs
 recipes/gottcha
-recipes/pepnovo
 recipes/ea-utils
 recipes/nextgenmap
 recipes/igor_vdj

diff --git a/recipes/abnumber/meta.yaml b/recipes/abnumber/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "0.3.8" %} # Remember to update sha256 below
+{% set version = "0.4.1" %} # Remember to update sha256 below
 
 package:
   name: abnumber
   version: '{{ version }}'
 
 source:
   url: https://github.com/prihoda/abnumber/archive/v{{ version }}.tar.gz
-  sha256: '9d811615800d479bb2ddd54996f1255806bd9ebc140407a54a0bc1790f9a8cee'
+  sha256: '240c7ccc1f85607ffdd0109f19761ab0488a059ae15e3ccd6066ef36c192a047'
 
 build:
   noarch: python

diff --git a/recipes/abpoa/meta.yaml b/recipes/abpoa/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.5.2" %}
+{% set version = "1.5.3" %}
 {% set name = "abPOA" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/yangao07/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 706f0ca0110f4974ae7b93157db560bb9beda4273d8c883fa6a03ccb19958149
+  sha256: bb97de2dbdec014f2fb24beb0c85fa0b2073f717f3b68639e1edd89239729e6c
 
 build:
   number: 0

diff --git a/recipes/afpdb/meta.yaml b/recipes/afpdb/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "afpdb" %}
-{% set version = "0.2.1" %}
+{% set version = "0.2.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 7e67c728a25c9ac565c79fa2615b0fd84ecbf9d661b1f575a863156e169fcf10
+  sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98
 
 build:
   number: 0

diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "AGAT" %}
-{% set version = "1.4.0" %}
-{% set sha256 = "d5e30db44b5d05ed51c606a823894c01c85c1ed85580148ad5473cb2f2b2ac77" %}
+{% set version = "1.4.1" %}
+{% set sha256 = "28dcdbcaac90164fbb75afdc41d34e3c997fbf0f46b0633e0ac653b3c6d2e409" %}
 
 package:
   name: "{{ name|lower }}"

diff --git a/recipes/agfusion/meta.yaml b/recipes/agfusion/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.4.1" %}
-{% set sha256 = "fd04591d764deeff69978f9d495c3baf854ccfba27366aa0ae4859ad85ca2c60" %}
+{% set version = "1.4.3" %}
+{% set sha256 = "0fdace7fad64713173cac049af3783bdb3db406d5a6dafd4cc0c1948d0724c8f" %}
 
 package:
   name: agfusion

diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.12.1" %}
+{% set version = "0.13.0" %}
 
 package:
   name: alignoth
@@ -14,7 +14,7 @@ build:
 
 source:
   url: https://github.com/alignoth/alignoth/archive/v{{ version }}.tar.gz
-  sha256: 9bbff76754c3f183b63047f44995e72a356b0628aee3638addbf6eb15e9a4813
+  sha256: a955e762d3593ac572424dbe775f1c554bb5ab10f391fb643c7d613cca416cc4
 
 requirements:
   build:

diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml
@@ -1,22 +1,22 @@
 {% set name="ampliconsuite" %}
-{% set AS_version="1.3.3" %}
+{% set AS_version="1.3.4" %}
 {% set AA_version="1.4.r2" %}
-{% set AC_version="1.2.0" %}
+{% set AC_version="1.2.1" %}
 
 package:
     name: {{ name }}
     version: {{ AS_version }}
 
 source:
-    # the sha256 sum is generated by doing
+    # the sha256 sum is generated by running the following on the release .tar.gz from Github.
     # $ wget -O- [URL] | shasum -a 256
     - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz
-      sha256: c29f159cb641068b5c38529eeb49a975d63b3369407603cf30f3d8cf49a380d5
+      sha256: 58f2b74eac0116e0830bceea66a854071e2a205b6f5b8e57ce61a0e358434a61
     - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz
       sha256: 987390d7a32a6c118e6c7fea5c7a5aba2db1b3e64fc3ece5f68f50c7cabf01fa
       folder: ampliconarchitectlib
     - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz
-      sha256: 85052324376756ca3558325dce45635276af3f41dd292601f673abaf9990790a
+      sha256: 5cd6b9f4e2239631b8f11adda99d8858c29de64cf6f1c7a38121946db06803c9
 
 build:
     noarch: python

diff --git a/recipes/apscale/meta.yaml b/recipes/apscale/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "apscale" %}
-{% set version = "2.0.2" %}
+{% set version = "2.0.3" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/apscale-{{ version }}.tar.gz
-  sha256: 13d32ad87c1cf2d161bd577421e848006de8bcbb831aab15e5ecd3a5b6fc4563
+  sha256: 52cf592e1446c958b781e5a134a2945989b33008805f46a071c97d073d330f00
 
 build:
   entry_points:

diff --git a/recipes/architeuthis/meta.yaml b/recipes/architeuthis/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "architeuthis" %}
-{% set version = "0.3.0" %}
+{% set version = "0.3.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/cdiener/{{ name }}/archive/{{ version }}.tar.gz
-  sha256: 63aba50c66188202debc822d0ded57d2398f5e4e9d8535f83a2c5e982bb4999f
+  sha256: 11b0e09785f23e479f3de55e12dfbe788c938a497a64c7293d8c4ce41d57ef2b
 
 build:
-  number: 1
+  number: 0
   script:
     - go build -v -ldflags "-w -s -X 'main.version={{ version }}'" -o $PREFIX/bin/architeuthis
   run_exports:

diff --git a/recipes/bactopia-py/meta.yaml b/recipes/bactopia-py/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "bactopia-py" %}
-{% set version = "1.1.1" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
-  sha256: a7e450658ca609d8fd93bc1beb343aa3fea76ac0cee06842f407cdc4d85299fa
+  sha256: bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1
 
 build:
   noarch: python
@@ -29,6 +29,7 @@ requirements:
     - pyyaml
     - requests
     - rich-click >=1.6.0
+    - tqdm
 
 test:
   imports:
@@ -42,6 +43,8 @@ test:
     - bactopia-prepare --help
     - bactopia-search --help
     - bactopia-summary --help
+    - bactopia-atb-formatter --help
+    - bactopia-atb-downloader --help
   requires:
     - pip
 

diff --git a/recipes/bactopia-qc/meta.yaml b/recipes/bactopia-qc/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.2" %}
+{% set version = "1.0.3" %}
 
 package:
   name: bactopia-qc
@@ -7,10 +7,12 @@ package:
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('bactopia-qc', max_pin='x.x') }}
 
 source:
   url: https://github.com/bactopia/bactopia-qc/archive/v{{version}}.tar.gz
-  sha256: e30768ecd3f46d84d36d2db8c931db83b350e988822eeb3594db4031e015c7e1
+  sha256: f1c07ee9aadd35cc9689070f236617afdc39f28210313675794e21a74f098244
 
 requirements:
   run:
@@ -27,7 +29,7 @@ requirements:
     - pigz
     - porechop >=0.2.4
     - python >=3.7,<3.11
-    - rasusa >=0.7.1
+    - rasusa >=1
     - rename
     - sed
 

diff --git a/recipes/bactopia-teton/meta.yaml b/recipes/bactopia-teton/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.4" %}
+{% set version = "1.1.1" %}
 
 package:
   name: bactopia-teton
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/bactopia/bactopia-teton/archive/v{{version}}.tar.gz
-  sha256: 648b476bcf15bc177df1a814d782d318ee6b78a38e2ccb8268c569cbd1576504
+  sha256: c62d0f74d5d4f48573af055424368de4ec4f88b744c7e3d451f818838f3b2da1
 
 requirements:
   run:
@@ -28,12 +28,14 @@ requirements:
     - pigz
     - python >=3.6,<3.11
     - sed
+    - sizemeup >=1.2.3
     - sra-human-scrubber >=2.2
 
 test:
   commands:
     - "bactopia-teton"
     - "kraken-bracken-summary.py --help"
+    - "teton-prepare.py --help"
 
 about:
   home: https://bactopia.github.io/

diff --git a/recipes/bactopia/meta.yaml b/recipes/bactopia/meta.yaml
@@ -1,23 +1,23 @@
 {% set name = "bactopia" %}
-{% set version = "3.0.1" %}
+{% set version = "3.1.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name, max_pin='x.x') }}
 
 source:
   url: https://github.com/bactopia/bactopia/archive/v{{version}}.tar.gz
-  sha256: f3f152294555c05ec37c20041385034b02a79a709d7801b07d2115f50115fa4a
+  sha256: a8134a5de2aa2e3d8131188420dadc034c5dcf4559c5c752148a103ddc47f463
 
 requirements:
   run:
-    - bactopia-py 1.0.9
+    - bactopia-py 1.1.1
     - conda >=22.11.0
     - coreutils
     - mamba >=1.1.0

diff --git a/recipes/baltic/meta.yaml b/recipes/baltic/meta.yaml
@@ -1,35 +1,38 @@
 {% set name = "baltic" %}
-{% set version = "0.2.2" %}
+{% set version = "0.3.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 095045aeb0f86f7668df5d7f163ab9fec30e59a564fc77c06b5cb756027a1e79
+  sha256: d7fd92d0a40840f15826416e5aaaa3b9e40db07df99f9d4add2eeaf683ae385d
 
 build:
   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
   noarch: python
+  run_exports:
+    - {{ pin_subpackage('baltic', max_pin="x.x") }}
 
 requirements:
   host:
     - pip
-    - python
+    - python >=3.5
   run:
     - matplotlib-base >=2.0.0
     - numpy >=1.16
-    - python
+    - python >=3.5
 
 test:
   imports:
     - baltic
 
 about:
   home: "https://github.com/evogytis/baltic"
-  license: GPL-3.0
+  license: GPL-3.0-or-later
   license_family: GPL3
   license_file: LICENSE 
-  summary: "Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees"
+  summary: "Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees."
+  dev_url: "https://github.com/evogytis/baltic"
diff --git a/recipes/bambamc/build.sh b/recipes/bambamc/build.sh
@@ -1,7 +1,12 @@
 #!/usr/bin/env bash
 
+set -xe
+
+# use newer config.guess and config.sub that support osx arm64
+cp ${RECIPE_DIR}/config.* .
+
 export C_INCLUDE_PATH=${PREFIX}/include
 export LIBRARY_PATH=${PREFIX}/lib
 ./configure --prefix=${PREFIX}
-make
+make -j ${CPU_COUNT}
 make install