Merge remote-tracking branch 'bioconda_origin/master' into saccharis

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/biobb_chemistry/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_chemistry" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.1" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: c4f3926a8a219410afa1e79feb84b71a2d1bb70bc0700039d52726853113b0e8
+  sha256: 585effae00b36a8ace8171c399b99afc9bf8103770caf341b6bff7ba7df1ee88
 
 build:
   number: 0

recipes/bubblegun/meta.yaml

@@ -0,0 +1,40 @@
+{% set name = "BubbleGun" %}
+{% set version = "1.1.9" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: "https://github.com/fawaz-dabbaghieh/bubble_gun/archive/refs/tags/v{{ version }}.tar.gz"
+  sha256: 005d61a1e5774dfec810e612c1b4c5ce6c8d15f80d131237590ef71f62704c94
+
+build:
+  number: 0
+  noarch: python
+  entry_points:
+    - BubbleGun=BubbleGun.main:main
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_compatible('BubbleGun', max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.6
+    - pip
+    - setuptools
+  run:
+    - python >=3.6
+
+test:
+  commands:
+    - BubbleGun -h
+
+about:
+  home: "https://github.com/fawaz-dabbaghieh/bubble_gun"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: 'BubbleGun is a tool for detecting bubbles and superbubbles in GFA graphs, and reports them and their nested structures.'
+  doc_url: "https://github.com/fawaz-dabbaghieh/bubble_gun/blob/v{{ version }}/README.md"
+  dev_url: "https://github.com/fawaz-dabbaghieh"

recipes/cmaple/build.sh

@@ -8,13 +8,16 @@ set -ex
 sed -i.bak 's/-mavx/-mno-avx -mno-avx2 -march=nocona -mtune=haswell/' CMakeLists.txt
 
 DCMAKE_ARGS=""
-if [ "$(uname)" == Darwin ]; then
+if [[ "$(uname)" == Darwin ]]; then
 	CC=$(which "$CC")
 	CXX=$(which "$CXX")
 	AR=$(which "$AR")
 	RANLIB=$(which "$RANLIB")
 	DCMAKE_ARGS=(-DCMAKE_C_COMPILER="${CC}" -DCMAKE_CXX_COMPILER="${CXX}"
 		-DCMAKE_CXX_COMPILER_AR="${AR}" -DCMAKE_CXX_COMPILER_RANLIB="${RANLIB}")
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
 fi
 
 case $(uname -m) in
@@ -27,10 +30,12 @@ aarch64)
 esac
 
 mkdir build
-cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" -G Ninja \
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release -G Ninja \
 	"${DCMAKE_ARGS[@]}" \
 	-DBUILD_GMOCK=OFF -DINSTALL_GTEST=OFF \
-	-Wno-dev -Wno-deprecated --no-warn-unused-cli
+	-Wno-dev -Wno-deprecated --no-warn-unused-cli \
+	"${CONFIG_ARGS}"
 
 VERBOSE=1 cmake --build build --target install -j ${JOBS}
 

recipes/cmaple/meta.yaml

@@ -1,19 +1,20 @@
 {% set name = "cmaple" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "68693229053d8c456028b7696ee39770ff55a3eaf3454d7087def08accbf0603" %}
+{% set version = "1.1.0" %}
+{% set sha256 = "72079ac3881840ce6a6d45603202a2ab9a399aa8ebaf51fbdcd85337696e4435" %}
+
 package:
   name: {{ name }}
   version: {{ version | replace("-", "_") }}
+
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
+
 source:
   - url: https://github.com/iqtree/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
     sha256: {{ sha256 }}
-    # Patch necessary to build on arm, can be removed with next release
-    patches:
-      - patch
+
 requirements:
   build:
     - {{ compiler('c') }}
@@ -24,6 +25,7 @@ requirements:
   host:
     - libgomp  # [linux]
     - llvm-openmp  # [osx]
+
 test:
   source_files:
     - example/input.fa
@@ -33,14 +35,16 @@ test:
     - cmaple-aa
     # Mulled builds don't work with source_files
     - cmaple -aln example/input.fa  # [osx]
+
 about:
   home: "https://github.com/iqtree/cmaple"
   dev_url: "https://github.com/iqtree/cmaple"
   doc_url: "https://github.com/iqtree/cmaple/wiki"
   license: "GPL-2.0"
   license_family: GPL2
   license_file: LICENSE
-  summary: "MAximum Parsimonious Likelihood Estimation in C/C++"
+  summary: "MAximum Parsimonious Likelihood Estimation in C/C++."
+
 extra:
   additional-platforms:
     - linux-aarch64