Merge branch 'master' into coptr_pythonVersion

recipes/aletsch/meta.yaml

@@ -1,16 +1,16 @@
 {% set name = "aletsch" %}
-{% set version = "1.1.2" %}
+{% set version = "1.1.3" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 source:
   url: "https://github.com/Shao-Group/aletsch/releases/download/v{{ version }}/aletsch-{{ version }}.tar.gz"
-  sha256: "b081cfcbd2f232dcddab4f9c6ce11f15f41e4319e1f977dd955cca240748d4b5"
+  sha256: "74e1b7e2ff2cb065d02f1e0d45d7e87ae332ccfcef86b6a32af88b2a7005c9f7"
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('aletsch', max_pin="x") }}
 

recipes/amplici/build.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ `uname` == "Darwin" ]]; then
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+    export CONFIG_ARGS=""
+fi
+
+cd src || exit 1
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_C_COMPILER="${CC}" \
+    -DCMAKE_C_FLAGS="${CFLAGS}" \
+    "${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v

recipes/amplici/meta.yaml

@@ -0,0 +1,46 @@
+{% set version = "2.2" %}
+
+package:
+  name: amplici
+  version: {{ version }}
+
+source:
+  url: https://github.com/DormanLab/AmpliCI/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 273362b5449ec29ff411d4c1aa5f89b1ec1eb361c8a9b69a4d89f4409fbdb70e
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("amplici", max_pin="x") }}
+
+requirements:
+  build:
+    - cmake
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - {{ compiler('fortran') }}
+  host:
+    - zlib
+
+about:
+  home: https://github.com/DormanLab/AmpliCI
+  license: BSD 3-Clause
+  license_family: BSD
+  license_file: LICENSE  
+  summary: "AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs."
+  dev_url: https://github.com/DormanLab/AmpliCI
+
+test:
+  commands:
+    - run_AmpliCI -h
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - xiyupeng
+  identifiers:
+    - biotools:amplici
+    - doi:10.1093/bioinformatics/btaa648

recipes/arcs/meta.yaml

@@ -1,17 +1,17 @@
-{% set version = "1.2.7" %}
+{% set version = "1.2.8" %}
 
 package:
   name: arcs
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('arcs', max_pin="x") }}
 
 source:
   url: https://github.com/bcgsc/arcs/releases/download/v{{ version }}/arcs-{{ version }}.tar.gz
-  sha256: 3162cff3286a033b494ace8050abc96d4083f846cafe921bb0122170f705eca8
+  sha256: 3393151980ee1e031ff47d32e2871745255a08e9e76f27657e868137b4ddd2df
 
 requirements:
   build:
@@ -43,4 +43,4 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
-    - osx-arm64
+    - osx-arm64

recipes/argo/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "argo" %}
-{% set version = "0.1.1" %}
+{% set version = "0.1.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 9ddc3bea602e3bdcd3518bb3ecd7795b680addaa513eff0fff83e1010ba4e253
+  sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ build:
 requirements:
   host:
     - pip
+    - setuptools
     - python >=3.7
   run:
     - python >=3.7
@@ -36,7 +37,7 @@ about:
   home: https://github.com/xinehc/argo
   license: MIT
   license_family: MIT
-  summary: 'Argo: species-resolved profiling of antibiotic resistant genes with long-read metagenomics'
+  summary: 'Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping'
 
 extra:
   recipe-maintainers:

recipes/argparse2tool/meta.yaml

@@ -1,28 +1,30 @@
 {% set name = "argparse2tool" %}
-{% set version = "0.4.9" %}
+{% set version = "0.5.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: ecd7142c1ce60bf9e1416443ce393907b7f99a9396a0530277c110dcb7106579
+  sha256: 8c6fbf68df690edf80f438b458e6da1f943254b0c4337ac2b732c567c67fde46
 
 build:
   number: 0
   entry_points:
     - argparse2tool_check_path = argparse2tool.check_path:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
+  run_exports:
+    - {{ pin_subpackage('argparse2tool', max_pin="x.x") }}
 
 requirements:
   host:
     - pip
     - python >=3
+    - setuptools
   run:
-    - click
-    - galaxyxml >=0.2.3
+    - galaxyxml >=0.4.6
     - jinja2
     - python >=3
 

recipes/ascat/build.sh

@@ -7,10 +7,4 @@ pushd ASCAT
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
 
-$R CMD INSTALL --build .
-
-# Add more build steps here, if they are necessary.
-
-# See
-# http://docs.continuum.io/conda/build.html
-# for a list of environment variables that are set during the build process.
+${R} CMD INSTALL --build . "${R_ARGS}"

recipes/ascat/meta.yaml

@@ -1,20 +1,22 @@
-{% set version = "3.1.1" %}
-{% set sha256 = "7d63c8bb8eb53f463732950f649db01f7055d89801438a2ac5933f16a9ba1042" %}
+{% set version = "3.2.0" %}
+{% set sha256 = "e866c1b4eec503bde643c6922bfc30c03cf2783e903072779d8b81819f17b547" %}
 
 package:
   name: ascat
   version: '{{ version }}'
 
 source:
-  url: https://github.com/Crick-CancerGenomics/ascat/archive/v{{ version }}.tar.gz
+  url: https://github.com/VanLoo-lab/ascat/archive/refs/tags/v{{ version }}.tar.gz
   sha256: '{{ sha256 }}'
 
 build:
-  number: 1
+  number: 0
   noarch: generic
   rpaths:
     - lib/R/lib/
     - lib/
+  run_exports:
+    - {{ pin_subpackage('ascat', max_pin="x") }}
 
 requirements:
   host:
@@ -38,15 +40,14 @@ requirements:
     - bioconductor-genomicranges
     - bioconductor-iranges
 
-
 test:
   commands:
     - $R -e "library(ASCAT)"
 
 about:
-  home: https://www.crick.ac.uk/research/a-z-researchers/researchers-v-y/peter-van-loo/software/
-  license: GPL-3.0
-  license_family: GPL
+  home: https://www.crick.ac.uk/research/a-z-researchers/researchers-v-y/peter-van-loo/software
+  license: GPL-3.0-or-later
+  license_family: GPL3
   summary: |
     ASCAT is a method to derive copy number profiles of tumour cells,
     accounting for normal cell admixture and tumour aneuploidy (Figure 1).
@@ -56,6 +57,7 @@ about:
     whole-genome allele-specific copy number profiles (the number of copies of
     both parental alleles for all SNP loci across the genome).
   dev_url: https://github.com/Crick-CancerGenomics/ascat
+  doc_url: https://github.com/VanLoo-lab/ascat/blob/v{{ version }}/README.md
 
 extra:
   identifiers:

recipes/aster/meta.yaml

@@ -1,13 +1,13 @@
-{% set version = "1.16" %}
+{% set version = "1.19" %}
 {% set name = "ASTER" %}
-{% set sha256 = "c6e80de483a0a59fc0d3a74465b1f793e773b9d79cbd20756c6766136ffbb1a7" %}
+{% set sha256 = "f6d7fd58297ab854a6c869ba5d6715d056a82df8254c0d6cba6d9a6db355f054" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('aster', max_pin="x") }}
 

recipes/bam2plot/meta.yaml

@@ -0,0 +1,48 @@
+{% set name = "bam2plot" %}
+{% set version = "0.3.6" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz
+  sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541
+
+build:
+  entry_points:
+    - bam2plot=bam2plot.main:cli
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('bam2plot', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - setuptools
+  run:
+    - python >=3.10
+    - pysam >=0.22.0
+    - seaborn >=0.13.2
+    - polars >=0.20.15
+    - mappy >=2.28
+    - pyfastx
+    - pyarrow
+    - mosdepth
+
+test:
+  imports:
+    - bam2plot
+  commands:
+    - bam2plot from_bam --help
+    - bam2plot from_reads --help
+    - bam2plot guci --help
+
+about:
+  home: https://github.com/willros/bam2plot
+  summary: Plot of coverage from bam file
+  license: GPL-3.0-only
+  license_file: LICENSE

recipes/bbmap/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "BBMap" %}
-{% set version = "39.10" %}
-{% set sha256 = "996aff05765ba5e64547f8a34c56da396ce7b18db96ffe7f1076f2d2f49c6148" %}
+{% set version = "39.11" %}
+{% set sha256 = "bcb80b109757a638d6c767b7ba785fde5111437f7025e0a93dce587cdfaa2795" %}
 
 package:
   name: {{ name|lower }}
@@ -19,13 +19,13 @@ requirements:
   build:
     - {{ compiler('c') }}
   host:
-    - openjdk >=7.0
+    - openjdk >=11.0.1
     - pbzip2
     - bzip2
     - samtools
     - patchelf  # [osx]
   run:
-    - openjdk >=7.0
+    - openjdk >=11.0.1
     - samtools
 
 test:

recipes/bftools/meta.yaml

@@ -1,18 +1,20 @@
-{% set version = "6.7.0" %}
-{% set sha256 = "7c013b23529d61280e04c3dd312401d7b71fb5892f5e7870f87d37bab5f3988f" %}
+{% set version = "8.0.0" %}
+{% set sha256 = "46c7c53595a2491adc76dc3b7d4089689e5c3817a9bb549a632d08ef137438e7" %}
 
 
 package:
   name: bftools
   version: '{{version}}'
 
 source:
-  url: "http://downloads.openmicroscopy.org/latest/bio-formats{{version}}/artifacts/bftools.zip"
+  url: https://downloads.openmicroscopy.org/bio-formats/{{ version }}/artifacts/bftools.zip
   sha256: '{{sha256}}'
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('bftools', max_pin="x.x") }}
 
 requirements:
   run:
@@ -21,6 +23,8 @@ requirements:
 test:
   commands:
     - bfconvert -version
+    - domainlist
+    - formatlist
 
 about:
   home: https://docs.openmicroscopy.org/bio-formats/{{version}}/users/comlinetools/index.html

recipes/bigtools/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "0.5.2" %}
+{% set version = "0.5.3" %}
 
 package:
   name: bigtools
@@ -11,7 +11,7 @@ build:
 
 source:
   url: https://github.com/jackh726/bigtools/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: "f5b50a4d717f93242541673bbdeb1fa67b8b9175b0f72d8ff5c52f1563b5cd4e"
+  sha256: "092100e9f32fa6b5a6414703d135c333aa6959bf3aa2d608ec54aacab92eb7fb"
 
 requirements:
   build: