Merge branch 'bioconda:master' into hsdecipher

bioconda · Sep 30, 2024 · bca1baa · bca1baa
2 parents 56a4894 + 82c0af1
commit bca1baa
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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/bactopia-teton/meta.yaml b/recipes/bactopia-teton/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.4" %}
+{% set version = "1.0.5" %}
 
 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: 4340da1ca721850564dcc05491ee396d1f9a1bbf662de5ede12fa29c50c1f3be
 
 requirements:
   run:
@@ -28,6 +28,7 @@ requirements:
     - pigz
     - python >=3.6,<3.11
     - sed
+    - sizemeup >=1.0.2
     - sra-human-scrubber >=2.2
 
 test:

diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.3.1" %}
-{% set sha256 = "db6b99456a334b958ba61fcfc6e717e5f22848342f99fecb1f6f2b0113165054" %}
+{% set version = "3.3.2" %}
+{% set sha256 = "6c6dcac689a2fb0f8142546aa9021bfd620fe484e724e4844a2d2e55c337747c" %}
 
 package:
   name: {{ name }}
@@ -21,7 +21,7 @@ build:
 
 requirements:
   host:
-    - python
+    - python <3.12
     - pip
   run:
     - conda-forge-pinning 2024.06.01.05.54.15

diff --git a/recipes/blaze2/meta.yaml b/recipes/blaze2/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "BLAZE2" %}
-{% set version = "2.4.0" %}
+{% set version = "2.5.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/shimlab/BLAZE/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: b4487873d1f4ae389feed54aa7d862ff3addc458c387d6fd0e3c9550c0a2037d
+  sha256: f47175997742562add1deb9524e468b6709e40c92f74165a1a0fe1897b2919fc
 
 build:
   number: 0

diff --git a/recipes/catfasta2phyml/meta.yaml b/recipes/catfasta2phyml/meta.yaml
@@ -1,14 +1,16 @@
 package:
   name: catfasta2phyml
-  version: "1.2.0"
+  version: "1.2.1"
 
 source:
-  url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v.1.2.0.tar.gz
-  sha256: f4ea5aef5aa21d15d84436262f06b79a004b7017ab7a433019fe903aec995fdb
+  url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v1.2.1.tar.gz
+  sha256: 2647985192b05df49e10bfce64d6843fe7916b0395199dfd2ac4f80910c5a91f
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('catfasta2phyml', max_pin="x") }}
 
 requirements:
   run:

diff --git a/recipes/cpstools/meta.yaml b/recipes/cpstools/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "cpstools" %}
-{% set version = "1.0.13" %}
-{% set sha256 = "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1" %}
 
 package:
   name: {{ name|lower }}
@@ -21,13 +21,14 @@ build:
 
 requirements:
   host:
-    - python >=3.10
+    - python >=3.9
     - poetry-core
     - pip
   run:
-    - python >=3.10.0
+    - python >=3.9
     - biopython >=1.84.0
     - numpy >=1.26.4
+    - tqdm >=4.66.5
 
 test:
   imports:

diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   skip: True  # [osx or py < 39]
-  number: 0
+  number: 1
   entry_points:
     - genomedata-close-data = genomedata._close_data:main
     - genomedata-erase-data = genomedata._erase_data:main
@@ -45,7 +45,7 @@ requirements:
     - hdf5
     - pytables >=3.4.3
     - pybigwig
-    - path.py
+    - path
     - textinput
     - bedtools
     - ucsc-bigwigtobedgraph >=377

diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "GToTree" %}
-{% set version = "1.8.6" %}
+{% set version = "1.8.7" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz
-  sha256: 1712d9e18f128bbeeb585b1528a8e207c3a36cc7f1dbb7df66416ec0278d5a9a
+  sha256: 2ec94fa0bbcfa98edca126ee3446ab7fa8982cd746604b371f74a125e3e44435
 
 build:
   number: 0

diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "gxf2bed" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: gxf2bed
   version: {{ version }}
 
 source:
   url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: ee500e08e8c94b2663ea511482d6520300cb81c9cbbb05a288563e4a808f5377
+  sha256: 1f8358a972bded0c4906bf03532ba4ee9f7fc6bf9b84063e4b25b98f37ced45f
 
 build:
   number: 0

diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "1.0.5" %}
-{% set sha256 = "c84a4e2436904f0cbea7126abf2a5f665a870735c8af786883e10f3f872bda28" %}
+{% set version = "1.0.8" %}
+{% set sha256 = "cc7e496ff82f00b56ef59aa2a04fa572a2025225b0558e0df144f166fade82d4" %}
 
 package:
   name: metabuli
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('metabuli', max_pin="x") }}
 

diff --git a/recipes/nanovar/meta.yaml b/recipes/nanovar/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "1.8.0" %}
+{% set version = "1.8.1" %}
 
 package:
   name: nanovar
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/n/nanovar/nanovar-{{ version }}.tar.gz
-  sha256: 966117fc5667639dee4910823481037dc451ee972b3afdf93786f3f736eb120b
+  sha256: c75159f86a4043f5ba37c4ea16b9c5953e44d7a1c1dd854de7928464bed83bc9
 
 build:
   skip: True  # [py2k or osx or py > 39]
@@ -23,7 +23,7 @@ requirements:
     - python
   run:
     - python
-    - numpy >=1.17.3
+    - numpy >=1.17.3, <2.0.0
     - scipy >=1.2.1
     - biopython >=1.82
     - pybedtools >=0.8.2

diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ont-modkit" %}
-{% set version = "0.4.0" %}
-{% set sha256 = "a4a304f00f350074b50fb3c71ab8756df0344e0f77a55c443aa48a91c42195bf" %}
+{% set version = "0.4.1" %}
+{% set sha256 = "45cd7d4ee69092db7412a15f02799c3118bf5fa4e40e193e30e8c65c4f762f79" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.0.5" %}
+{% set version = "2.0.6" %}
 
 package:
   name: parsnp
   version: '{{version}}'
 
 source:
   url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz"
-  sha256: 1d23695d0d624fa17e02c43b1d730200e526c17a48615593f75ee8fc35402489
+  sha256: cde5fb488418764e87942afa747002d01d35e80d7c3a44a71bb2d1bd4d69ed0c
 
 build:
   number: 0

diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.181" %}
+{% set version = "1.2.185" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 6025ec0898d20ea83593144619b1c94b5f99b46955205a74537b97270924ce7f
+  sha256: 9525f0548dd11df88b33845ecf51d17ee9c2c5675a0723ebf5c25c586c58e598
 
 build:
   number: 0

diff --git a/recipes/pytximport/meta.yaml b/recipes/pytximport/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pytximport" %}
-{% set version = "0.8.0" %}
+{% set version = "0.9.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pytximport-{{ version }}.tar.gz
-  sha256: 18bdf4fbcd78092bba18f6941f5640a937b4f0230c30c2e8fca38ce207b3840b
+  sha256: f311705a71faa095d7e65de63235df55c805fbab4fbea10010fdae11014b3c95
 
 build:
   noarch: python

diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml
@@ -1,38 +1,37 @@
-{% set version="1.3.0" %}
+{% set version = "1.3.1" %}
 
 package:
   name: quatradis
   version: {{ version }}
 
 source:
   url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 8634c61c93073028fc35df46b3d1337e7716924051c336a12172c65e1adb2e74
+  sha256: 0c05f40e14391b5044aa014cce345e43238ff01d06edfc72258f8608d3796590
 
 build:
   number: 0
-  script: python -m pip install -v --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation --no-cache-dir .
   run_exports:
-    - {{ pin_subpackage('quatradis', max_pin="x.x") }}
+    - {{ pin_subpackage('quatradis', max_pin="x") }}
 
 requirements:
   build:
     - {{ compiler('c') }}
   host:
-    - python =3.10
-    - cython >=0.20.1
+    - python
+    - cython
     - pip
   run:
-    - python =3.10
-    - cython
+    - python
     - setuptools  # for pkg_resources
+    - cython
     - biopython
     - pysam >=0.18.0
     - matplotlib-base
     - numpy
     - scipy
-    - dendropy
-    - seaborn
-    - graphviz
+    - dendropy ==4.6
+    - seaborn-base
     - python-graphviz
     - pandas
     - htslib
@@ -43,7 +42,7 @@ requirements:
     - bwa
     - samtools
     - minimap2
-    - snakemake
+    - snakemake-minimal
     - snakeviz
 
 test:
@@ -56,6 +55,7 @@ about:
   license_family: GPL3
   license_file: LICENSE
   summary: 'A set of tools to analyse the output from TraDIS analyses'
+  dev_url: https://github.com/quadram-institute-bioscience/QuaTradis
 
 extra:
   skip-lints:
@@ -66,5 +66,5 @@ extra:
     - sbastkowski
     - maplesond
     - thanhleviet
-  doi:
-    - 10.1093/bioinformatics/btw022
+  identifiers:
+    - doi:10.1093/bioinformatics/btw022
diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '0.4.3' %}
+{% set version = '0.4.4' %}
 
 package:
   name: r-diffcorr
@@ -8,7 +8,7 @@ source:
   url:
     - {{ cran_mirror }}/src/contrib/DiffCorr_{{ version }}.tar.gz
     - {{ cran_mirror }}/src/contrib/Archive/DiffCorr/DiffCorr_{{ version }}.tar.gz
-  sha256: b0d811cbd78eb69484fb184522cc358d9ad56235b85ee56bef22fc3c1d2df3f3
+  sha256: c729fe399aceaf3afb975777ff3483e5d557d9b55b33fe5803bdb8949ff33b17
 
 build:
   number: 0

diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "seqfu" %}
-{% set version = "1.22.0" %}
-{% set sha256 = "e1b9032caab8e2effcc5a075b372c2fae636494b06e3bf2f30086c8d39fb5281" %}
+{% set version = "1.22.2" %}
+{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/sizemeup/build.sh b/recipes/sizemeup/build.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin ${PREFIX}/share/sizemeup
+
+# Install sizemup library
+$PYTHON -m pip install --no-deps --ignore-installed -vv .
+
+# move main executable, and replace with wrapper
+chmod 755 bin/sizemeup-bioconda
+mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main
+cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup
+
+# Copy genome size database (~100kb)
+cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup