Merge branch 'master' into bump/starfish

bioconda · Oct 28, 2024 · e6fcaf5 · e6fcaf5
2 parents f17315a + ff969da
commit e6fcaf5
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Showing 27 changed files with 188 additions and 96 deletions.
diff --git a/.github/workflows/PR.yml b/.github/workflows/PR.yml
@@ -135,14 +135,8 @@ jobs:
         with:
           name: linux-packages
           path: |
-            /tmp/artifacts/packages
+            /tmp/artifacts
 
-      - name: Archive images 
-        uses: actions/upload-artifact@v4
-        with:
-          name: docker-images
-          path: |
-            /tmp/artifacts/images
 
   build-osx-64:
     name: OSX-64 Tests
@@ -214,7 +208,7 @@ jobs:
         with:
           name: osx-packages
           path: |
-            /tmp/artifacts/packages
+            /tmp/artifacts
 
   # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
   # build_and_test-osx-arm64:

diff --git a/azure-pipeline.yml b/azure-pipeline.yml
@@ -1,6 +1,7 @@
 # Disable Azure checks in favor of GitHub Actions due to memory issues
 # pr:
 #   autoCancel: true
+pr: none
 trigger: none
 # trigger: 
   # branches:

diff --git a/recipes/crabs/meta.yaml b/recipes/crabs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "crabs" %}
-{% set version = "1.0.5" %}
-{% set sha256 = "f948244c3b148e7c23b89f7aab68e28149504c60075f1e731e07a05fbd66d8f5" %}
+{% set version = "1.0.6" %}
+{% set sha256 = "8cbb930cd34aab5e7b7edca3403686ce9c15fddaf72fcdb7719a336644c22289" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml
@@ -1,8 +1,8 @@
 {% set user = "USDA-VS" %}
 {% set name = "GenoFLU" %}
 
-{% set version = "1.04" %}
-{% set sha256 = "f8dabd01e5f0fe00443b8991bf31dca38aa4d0064a564fb237dc4e9f0f1eec31" %}
+{% set version = "1.05" %}
+{% set sha256 = "af63053347082cd9fcfeab1ea4bff9ce9340ebbef636e509a72c9e7f4c56be3e" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/libgff/build.sh b/recipes/libgff/build.sh
@@ -0,0 +1,16 @@
+#!/bin/bash
+
+export M4="${BUILD_PREFIX}/bin/m4"
+
+if [[ `uname` == "Darwin" ]]; then
+	export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+	export CONFIG_ARGS=""
+fi
+
+cmake -S . -B build -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+	-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
+	-DCMAKE_CXX_FLAGS="${CXXFLAGS}" \
+	"${CONFIG_ARGS}"
+
+cmake --build build --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/libgff/meta.yaml b/recipes/libgff/meta.yaml
@@ -0,0 +1,42 @@
+{% set name = "libgff" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/COMBINE-lab/libgff/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('libgff', max_pin='x') }}
+
+requirements:
+  build:
+    - make
+    - cmake
+    - {{ compiler('cxx') }}
+  host:
+    - bzip2
+    - zlib
+    - xz
+
+test:
+  commands:
+    - "ls ${PREFIX}/lib/libgff.a"
+
+about:
+  home: https://github.com/COMBINE-lab/libgff
+  license: MIT
+  license_family: MIT
+  summary: 'A simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase.'
+  dev_url: https://github.com/COMBINE-lab/libgff
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/lima/meta.yaml b/recipes/lima/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "lima" %}
-{% set version = "2.9.0" %}
+{% set version = "2.12.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/PacificBiosciences/barcoding/releases/download/v{{ version }}/lima.tar.gz
-  sha256: a13437bc7a90ab5df3c19eac44384de2a14370d0391586b5aa63a6478f9c2c53
+  sha256: 7e6ac701b8625867bf7486583e741cc86a58e8c91384826613067364229e5627
 
 build:
-  number: 1
+  number: 0
   skip: True  # [osx]
   binary_relocation: False
   run_exports:
@@ -31,5 +31,5 @@ extra:
     - armintoepfer
     - pb-dseifert
   skip-lints:
-    #repackaged binary
+    #repackaged binary 
     - should_be_noarch_generic
diff --git a/recipes/masurca/meta.yaml b/recipes/masurca/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "masurca" %}
-{% set version = "4.1.1" %}
+{% set version = "4.1.2" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/alekseyzimin/masurca/releases/download/v{{ version }}/MaSuRCA-{{ version }}.tar.gz
-  sha256: 8758f6196bf7f57e24e08bda84abddfff08feb4cea204c0eb5e1cb9fe8198573
+  sha256: 68d17e80295a242733bd875ef918f1af4fb3bb8ade29112e1a76cedc92dd619a
   patches:
     - 0001-install.sh.patch
 
 build:
-  number: 2
+  number: 0
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}

diff --git a/recipes/miniprot/build.sh b/recipes/miniprot/build.sh
@@ -1,6 +1,8 @@
 #!/bin/bash
 
-make CC=$CC CFLAGS="$CFLAGS -I$PREFIX/include" LIBS="$LDFLAGS -L$PREFIX/lib -lpthread -lz -lm"
+set -xe
+
+make -j"${CPU_COUNT}" CC=$CC CFLAGS="$CFLAGS -I$PREFIX/include" LIBS="$LDFLAGS -L$PREFIX/lib -lpthread -lz -lm"
 
 if [ ! -d $PREFIX/bin ] ; then
 	mkdir -p $PREFIX/bin

diff --git a/recipes/miniprot/meta.yaml b/recipes/miniprot/meta.yaml
@@ -7,7 +7,7 @@ package:
   version: "{{ version }}"
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -35,3 +35,8 @@ about:
   summary: |
     Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
     It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/mycotools/meta.yaml b/recipes/mycotools/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "mycotools" %}
-{% set version = "0.32.4" %}
+{% set version = "0.32.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mycotools-{{ version }}.tar.gz
-  sha256: 9269affbc752d5c378e0d7f206220c8bedeb96f2064d8783957b07de210c5666 
+  sha256: e886c43b5faffb4d788a23f6016d146724c85ec8c9fc57ab3e0fcc24840c30b7 
 
 build:
   number: 0

diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.04.4" %}
-{% set sha256 = "03bf3ad5018ce2eac7bf7836140475a1fda529d800503aa39565fc6c77a40bfd" %}
+{% set version = "24.10.0" %}
+{% set sha256 = "e848918fb9b85762822c078435d9ff71979a88cccff81ce5babd75d5eee52fe6" %}
 
 package:
   name: nextflow

diff --git a/recipes/perl-datetime-locale/meta.yaml b/recipes/perl-datetime-locale/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "perl-datetime-locale" %}
-{% set version = "1.43" %}
-{% set sha256 = "6c859c17cf274749dfc2c6aaf6bf4b492b605fabdddd23712efbbd5caf601de1" %}
+{% set version = "1.44" %}
+{% set sha256 = "12a584a4a43c46114cd41ab6981be3609588604a906463fe4f844bb88a31c2de" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/DateTime-Locale-1.43.tar.gz
+  url: https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/DateTime-Locale-1.44.tar.gz
   sha256: {{ sha256 }}
 
 build:

diff --git a/recipes/perl-term-table/meta.yaml b/recipes/perl-term-table/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "perl-term-table" %}
-{% set version = "0.022" %}
-{% set sha256 = "b9dbdacfa7362846e3c4a100081832db9da74b7356828ef9d92869c44642e0b8" %}
+{% set version = "0.023" %}
+{% set sha256 = "e45042face1801d99c0bead6ca5f363a34e0e055f4fe6b0ccb208de481072bd3" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
-  url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.022.tar.gz
+  url: https://cpan.metacpan.org/authors/id/E/EX/EXODIST/Term-Table-0.023.tar.gz
   sha256: {{ sha256 }}
 
 build:

diff --git a/recipes/prodigal-gv/build.sh b/recipes/prodigal-gv/build.sh
@@ -1,8 +1,10 @@
 #!/bin/sh
 
+set -xe
+
 # the executable is not installed in $PREFIX though
 # make install prefix=$PREFIX
 
-make CC=$CC
+make -j"${CPU_COUNT}" CC=$CC
 mkdir -p $PREFIX/bin
 cp $PKG_NAME $PREFIX/bin
diff --git a/recipes/prodigal-gv/meta.yaml b/recipes/prodigal-gv/meta.yaml
@@ -9,7 +9,9 @@ source:
   sha256: 1fb40a8ae204ce2f41a413edb1edf5b8f22c28c2812320e2807ab48f8e8ce795
 
 build:
-  number: 2
+  number: 3
+  run_exports:
+    - {{ pin_subpackage('prodigal-gv', max_pin="x") }}
 
 requirements:
   build:
@@ -26,5 +28,11 @@ test:
 
 about:
   home: https://github.com/apcamargo/prodigal-gv
-  license: GPL v3
+  license: GPL-3.0-only
+  license_file: LICENSE
   summary: A fork of Prodigal meant to improve gene calling for giant viruses
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/sainsc/meta.yaml b/recipes/sainsc/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "sainsc" %}
-{% set version = "0.2.0" %}
+{% set version = "0.2.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/sainsc-{{ version }}.tar.gz
-  sha256: af964871f73b31177cf1a31844b6c40323384e0bd3c97ab2520ecbec23036d72
+  sha256: f710579c01809110c280bee838607fc6b961ca2f27b54aa7d431e25fe97b3872
 
 build:
   script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir

diff --git a/recipes/samshee/meta.yaml b/recipes/samshee/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "samshee" %}
-{% set version = "0.2.1" %}
+{% set version = "0.2.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://files.pythonhosted.org/packages/82/fa/895448adfc9be87b7af0a46b5c84eeae752d685966eba02d572e5c670f08/samshee-0.2.1.tar.gz
-  sha256: e85d9363de533dab91e3190c52eda9034cbaf1e53c03f0b33f4f9b433e800b76
+  url: https://files.pythonhosted.org/packages/38/04/edcd9859eb00dd3b0258aba128890d7d537b72e227b96a5f19837b54afd9/samshee-0.2.2.tar.gz
+  sha256: 360427adb2d3913c3eca4d97ff55933a51dcb3d7d82559c44d9323f69e98addc
 
 build:
   noarch: python

diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ShortStack" %}
-{% set version = "4.1.0" %}
-{% set sha256 = "f138672d1f564cdd9dffe384bc84ca01bbd67b8e76a9d9f030b47a0e478f3fe1" %}
+{% set version = "4.1.1" %}
+{% set sha256 = "24f0c259f3adce25637a7586bd8c7dae59f32df4d6fb2c974b57ad5506da2158" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/ucsc-bedgraphtobigwig/build.sh b/recipes/ucsc-bedgraphtobigwig/build.sh
@@ -9,13 +9,13 @@ export INCLUDE_PATH="${PREFIX}/include"
 export LIBRARY_PATH="${PREFIX}/lib"
 export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
 export CFLAGS="${CFLAGS} -O3 ${LDFLAGS}"
-export CXXFLAGS="${CXXFLAGS} -I${PREFIX}/include ${LDFLAGS}"
+export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}"
 export L="${LDFLAGS}"
 mkdir -p "${BINDIR}"
 (cd kent/src/lib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/htslib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/jkOwnLib && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/hg/lib && make USE_HIC=0 CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
 (cd kent/src/utils/bedGraphToBigWig && make CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" -j "${CPU_COUNT}")
-cp bin/bedGraphToBigWig "${PREFIX}/bin"
-chmod 0755 "${PREFIX}/bin/bedGraphToBigWig"
+chmod 0755 bin/bedGraphToBigWig
+mv bin/bedGraphToBigWig "${PREFIX}/bin"
diff --git a/recipes/ucsc-bedgraphtobigwig/include.macos.patch b/recipes/ucsc-bedgraphtobigwig/include.macos.patch
@@ -0,0 +1,27 @@
+--- a/kent/src/inc/common.mk	2017-11-07 17:46:00.000000000 -0500
++++ b/kent/src/inc/common.mk	2017-11-13 17:44:51.017090255 -0500
+@@ -17,7 +17,7 @@
+ endif
+
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib -I${PREFIX}/include
+
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+--- a/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
++++ b/kent/src/hg/lib/straw/makefile	2022-10-26 12:00:00.000000000 +0100
+@@ -1,4 +1,4 @@
+-KENT_INC=-I../../../inc
++KENT_INC=-I../../../inc -I${PREFIX}/include
+
+ straw: straw.o cStraw.o
+ 	ld -r -o ../straw.o straw.o cStraw.o
+--- a/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
++++ b/kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed	2018-06-06 02:23:56.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2.7
++#!/usr/bin/env python
+ # expMatrixToBarchartBed
+ """
+ Generate a barChart bed6+5 file from a matrix, meta data, and coordinates.