diff --git a/recipes/arcs/meta.yaml b/recipes/arcs/meta.yaml index a9d5122b1c4c3..21f64964882dd 100644 --- a/recipes/arcs/meta.yaml +++ b/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 \ No newline at end of file + - osx-arm64 diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml index 321d4a53e99df..3378a76c20d47 100644 --- a/recipes/argo/meta.yaml +++ b/recipes/argo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "argo" %} -{% set version = "0.1.1" %} +{% set version = "0.1.2" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: 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: diff --git a/recipes/argparse2tool/meta.yaml b/recipes/argparse2tool/meta.yaml index 6ecb346391010..651f50d085b75 100644 --- a/recipes/argparse2tool/meta.yaml +++ b/recipes/argparse2tool/meta.yaml @@ -1,5 +1,5 @@ {% set name = "argparse2tool" %} -{% set version = "0.4.9" %} +{% set version = "0.5.2" %} package: name: "{{ name|lower }}" @@ -7,22 +7,24 @@ package: 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 diff --git a/recipes/aspera-cli/build.sh b/recipes/aspera-cli/build.sh index 37603d593282b..efc2cd7bd20db 100644 --- a/recipes/aspera-cli/build.sh +++ b/recipes/aspera-cli/build.sh @@ -7,7 +7,7 @@ mkdir -p $GEM_HOME gem build aspera-cli.gemspec gem install --install-dir $GEM_HOME --bindir $GEM_HOME/bin ${PKG_NAME}-${PKG_VERSION}.gem gem_path=$GEM_HOME/gems/${PKG_NAME}-${PKG_VERSION} -cp -r $SRC_DIR/* $gem_path +cp -rf $SRC_DIR/* $gem_path rm $gem_path/{conda_build,build_env_setup}.sh tail -n+3 bin/ascli > $gem_path/bin/ascli tail -n+3 bin/asession > $gem_path/bin/asession @@ -25,9 +25,6 @@ EOF echo "$(cat header.txt $gem_path/bin/ascli)" > $gem_path/bin/ascli echo "$(cat header.txt $gem_path/bin/asession)" > $gem_path/bin/asession -ln -s $gem_path/bin/* $PREFIX/bin +ln -sf $gem_path/bin/* $PREFIX/bin -export ASCLI_HOME="$PREFIX/etc/aspera" -ascli conf ascp install && ascli config ascp info -cp $ASCLI_HOME/aspera-license . -ln -s $ASCLI_HOME/{ascp,aspera-license} $PREFIX/bin \ No newline at end of file +ascli conf ascp install && ascli config ascp info diff --git a/recipes/aspera-cli/meta.yaml b/recipes/aspera-cli/meta.yaml index 1004a29c34209..cd0e7cc0d44d1 100644 --- a/recipes/aspera-cli/meta.yaml +++ b/recipes/aspera-cli/meta.yaml @@ -1,5 +1,5 @@ {% set name = "aspera-cli" %} -{% set version = "4.14.0" %} +{% set version = "4.19.0" %} package: name: "{{ name|lower }}" @@ -7,17 +7,15 @@ package: source: - url: https://github.com/IBM/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: b46df368df71ad926605e85ea4b61b9e48335cce8be31ac04d97ee6f71109f03 + sha256: e4f9eb47510094132ff02960764254dfc322f1a16c9ad2b8abc60a54e5e21da1 build: noarch: generic - number: 1 + number: 0 run_exports: - {{ pin_subpackage('aspera-cli', max_pin="x") }} requirements: - build: - - ruby >=3 host: - ruby >=3 run: @@ -26,16 +24,15 @@ requirements: test: commands: - ascli -h - - ascp -h about: - home: https://github.com/IBM/aspera-cli - license: Apache-2.0 - license_file: - - LICENSE - - aspera-license - summary: "Command Line Interface for IBM Aspera products" - dev_url: https://github.com/IBM/aspera-cli + home: "https://github.com/IBM/aspera-cli" + license: "Apache-2.0" + license_file: LICENSE + license_family: APACHE + summary: "Command Line Interface for IBM Aspera products." + dev_url: "https://github.com/IBM/aspera-cli" + doc_url: "https://www.rubydoc.info/gems/aspera-cli" extra: recipe-maintainers: diff --git a/recipes/bam2plot/meta.yaml b/recipes/bam2plot/meta.yaml new file mode 100644 index 0000000000000..d11123a8715d4 --- /dev/null +++ b/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 diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index a69855905a211..3bb585ba8e733 100644 --- a/recipes/bbmap/meta.yaml +++ b/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: diff --git a/recipes/bftools/meta.yaml b/recipes/bftools/meta.yaml index 5d716cca12527..cba3893650909 100644 --- a/recipes/bftools/meta.yaml +++ b/recipes/bftools/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "6.7.0" %} -{% set sha256 = "7c013b23529d61280e04c3dd312401d7b71fb5892f5e7870f87d37bab5f3988f" %} +{% set version = "8.0.0" %} +{% set sha256 = "46c7c53595a2491adc76dc3b7d4089689e5c3817a9bb549a632d08ef137438e7" %} package: @@ -7,12 +7,14 @@ package: 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 diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml index 17755ee4702be..184c9e06805c0 100644 --- a/recipes/biobb_chemistry/meta.yaml +++ b/recipes/biobb_chemistry/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_chemistry" %} -{% set version = "5.0.0" %} +{% set version = "5.0.2" %} package: name: '{{ name|lower }}' @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c4f3926a8a219410afa1e79feb84b71a2d1bb70bc0700039d52726853113b0e8 + sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05 build: - number: 0 + number: 1 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" run_exports: @@ -22,13 +22,13 @@ requirements: - setuptools - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools >=22.5 + - ambertools ==22.5 - acpype >=2023.10.27 run: - python >=3.9 - biobb_common ==5.0.0 - openbabel ==3.1.1 - - ambertools >=22.5 + - ambertools ==22.5 - acpype >=2023.10.27 test: imports: diff --git a/recipes/bioblend/meta.yaml b/recipes/bioblend/meta.yaml index 1211834359a86..d1fd47ce9461f 100644 --- a/recipes/bioblend/meta.yaml +++ b/recipes/bioblend/meta.yaml @@ -1,5 +1,5 @@ {% set name = "bioblend" %} -{% set version = "1.3.0" %} +{% set version = "1.4.0" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz - sha256: e72318e10c29a81c16281d25aaac00989a07fc2900be7479137964232cc4a507 + sha256: 175d49d288e27d132ff59c870551c87cd95d7747be55ab94807c563291a3fa1d build: number: 0 @@ -22,6 +22,7 @@ requirements: host: - python >=3.8 - pip + - setuptools run: - python >=3.8 - requests >=2.20.0 @@ -66,7 +67,7 @@ test: about: home: "https://github.com/galaxyproject/bioblend" license: MIT - summary: 'A Python library for interacting with the Galaxy API' + summary: 'A Python library for interacting with the Galaxy API.' license_family: MIT license_file: LICENSE doc_url: "https://bioblend.readthedocs.org/" diff --git a/recipes/cat/build.sh b/recipes/cat/build.sh index 5f93e3be2391b..712695498a8af 100644 --- a/recipes/cat/build.sh +++ b/recipes/cat/build.sh @@ -6,7 +6,6 @@ outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir mkdir -p $PREFIX/bin - mv CAT_pack $outdir -ln -s $outdir/CAT_pack/CAT $PREFIX/bin +ln -s $outdir/CAT_pack/CAT_pack $PREFIX/bin diff --git a/recipes/cat/meta.yaml b/recipes/cat/meta.yaml index 81e3fc1cbdc4b..8b24d8e78fd01 100644 --- a/recipes/cat/meta.yaml +++ b/recipes/cat/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "5.3" %} -{% set sha256 = "2893ee18b0d5b24a291edd7d8ca1738d40ea189d18ba0fb7aad3e38973a787e7" %} +{% set version = "6.0.1" %} +{% set sha256 = "189707d8a0f6fa3ce50ed5fd5e9955b97119b514d38a190d393a701ec652f8fc" %} package: name: cat version: {{ version }} source: - url: https://github.com/dutilh/CAT/archive/v{{ version }}.tar.gz + url: https://github.com/MGXlab/CAT_pack/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} build: @@ -14,19 +14,22 @@ build: noarch: generic run_exports: - {{ pin_subpackage("cat", max_pin="x") }} + requirements: run: - - python 3 + - python >=3 - diamond - prodigal test: commands: - - CAT prepare --help + - CAT_pack prepare -h about: summary: | CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) - home: https://github.com/dutilh/CAT + home: https://github.com/MGXlab/CAT_pack license: MIT + license_family: MIT license_file: LICENSE.md + dev_url: https://github.com/MGXlab/CAT_pack diff --git a/recipes/cd-hit/build.sh b/recipes/cd-hit/build.sh index e1aab78924f19..87fadaf02c43c 100644 --- a/recipes/cd-hit/build.sh +++ b/recipes/cd-hit/build.sh @@ -1,26 +1,28 @@ -#!/bin/sh +#!/bin/bash -export CFLAGS="-I$PREFIX/include" -export CPPFLAGS="-I$PREFIX/include" -export CXXFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" +mkdir -p $PREFIX/bin + +export CFLAGS="${CFLAGS} -O3" +export CPPFLAGS="${CPPFLAGS} -I$PREFIX/include" +export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include" +export LDFLAGS="${LDFLAGS} -L$PREFIX/lib" export CPATH=${PREFIX}/include sed -i.bak 's/^CC =$//g' Makefile sed -i.bak 's/^#LDFLAGS.*//g' Makefile - +rm -rf *.bak if [[ "$OSTYPE" == "darwin"* ]]; then #Lines below is commented out until fix provided for OPENMP support on OS X for this program CCFLAGS="$CCFLAGS -Wl,-rpath ${PREFIX}/lib -L${PREFIX}/lib -I${PREFIX}/include -fopenmp" sed -i.bak 's/CCFLAGS = -fopenmp/CCFLAGS += -fopenmp/g' Makefile + rm -rf *.bak LDFLAGS="$LDFLAGS -stdlib=libc++" make CC=$CXX openmp=no MAX_SEQ=1000000 else make CC=$GXX MAX_SEQ=1000000 fi - -mkdir -p $PREFIX/bin -make install PREFIX=$PREFIX/bin + +make install PREFIX="$PREFIX/bin" diff --git a/recipes/cd-hit/cd-hit.patch b/recipes/cd-hit/cd-hit.patch new file mode 100644 index 0000000000000..29ac6a70fd2ec --- /dev/null +++ b/recipes/cd-hit/cd-hit.patch @@ -0,0 +1,1093 @@ +diff --git a/FET.pl b/FET.pl +index 6db320f..bb56529 100755 +--- a/FET.pl ++++ b/FET.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Storable; + use strict; +diff --git a/cd-hit-2d-para.pl b/cd-hit-2d-para.pl +index 3cab955..e0c43c7 100755 +--- a/cd-hit-2d-para.pl ++++ b/cd-hit-2d-para.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # ============================================================================= + # CD-HIT + # http://cd-hit.org/ +diff --git a/cd-hit-auxtools/cd-hit-dup-PE-out.pl b/cd-hit-auxtools/cd-hit-dup-PE-out.pl +index bfe5af3..f035229 100755 +--- a/cd-hit-auxtools/cd-hit-dup-PE-out.pl ++++ b/cd-hit-auxtools/cd-hit-dup-PE-out.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $script_name = $0; + my $script_dir = $0; +diff --git a/cd-hit-clstr_2_blm8.pl b/cd-hit-clstr_2_blm8.pl +index 42f1e57..cb75ffb 100755 +--- a/cd-hit-clstr_2_blm8.pl ++++ b/cd-hit-clstr_2_blm8.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # + + my $rep; +@@ -23,7 +23,10 @@ while($ll=<>){ + else { + push(@non_reps, $id); + my @lls = split(/\s+/, $ll); +- my ($a, $iden) = split(/\//, $lls[-1]); ++ # my ($a, $iden) = split(/\//, $lls[-1]); #### bug, with cd-hit-est-2d, there are +/- sign e.g. 10:1029:30:1042/+/97.35% ++ my @mms = split(/\//, $lls[-1]); ++ my $a = $mms[0]; ++ my $iden = $mms[-1]; + chop($iden); ### removing % sign + my ($qb, $qe, $sb, $se) = split(/:/, $a); + my $alnln = $qe-$qb+1; +diff --git a/cd-hit-div.pl b/cd-hit-div.pl +index e349394..db8d942 100755 +--- a/cd-hit-div.pl ++++ b/cd-hit-div.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #not like cd-hit-div, this script do not sort input + #or throw away seq +diff --git a/cd-hit-para.pl b/cd-hit-para.pl +index 33f1a1b..6ee3ca1 100755 +--- a/cd-hit-para.pl ++++ b/cd-hit-para.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # ============================================================================= + # CD-HIT + # http://cd-hit.org/ +diff --git a/clstr2tree.pl b/clstr2tree.pl +index 73fd37a..56d9fe2 100755 +--- a/clstr2tree.pl ++++ b/clstr2tree.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $clstr = shift; + $fr = shift; # for nr80.clstr $fr = 0.8 +diff --git a/clstr2txt.pl b/clstr2txt.pl +index 902b083..127537e 100755 +--- a/clstr2txt.pl ++++ b/clstr2txt.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $no = 0; + my $clstr_no = ""; +diff --git a/clstr2xml.pl b/clstr2xml.pl +index 10d828c..ba8264a 100755 +--- a/clstr2xml.pl ++++ b/clstr2xml.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...] + #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results +diff --git a/clstr_cut.pl b/clstr_cut.pl +index 498f180..ae0264c 100755 +--- a/clstr_cut.pl ++++ b/clstr_cut.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #keep only top $no proteins in cluster + +diff --git a/clstr_list.pl b/clstr_list.pl +index 9c6639b..b997402 100755 +--- a/clstr_list.pl ++++ b/clstr_list.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Storable; + use strict; +diff --git a/clstr_list_sort.pl b/clstr_list_sort.pl +index e0d20d8..a9bd588 100755 +--- a/clstr_list_sort.pl ++++ b/clstr_list_sort.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Storable; + use strict; +diff --git a/clstr_merge.pl b/clstr_merge.pl +index 3fe108e..9186777 100755 +--- a/clstr_merge.pl ++++ b/clstr_merge.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # the order of clusters need to be identical + my ($master_clstr, @clstr) = @ARGV; +diff --git a/clstr_merge_noorder.pl b/clstr_merge_noorder.pl +index f8acdfc..0852aee 100755 +--- a/clstr_merge_noorder.pl ++++ b/clstr_merge_noorder.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + # order of clusters don't need to be the same + # but then I have to read everything into memory +diff --git a/clstr_quality_eval.pl b/clstr_quality_eval.pl +index 62f2a3d..060ab01 100755 +--- a/clstr_quality_eval.pl ++++ b/clstr_quality_eval.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + ## calculate the sensitivity and specificity of clusters + ## if the input fasta file has pre-defined classification term +diff --git a/clstr_quality_eval_by_link.pl b/clstr_quality_eval_by_link.pl +index 8fba8df..140c05c 100755 +--- a/clstr_quality_eval_by_link.pl ++++ b/clstr_quality_eval_by_link.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + ## calculate the sensitivity and specificity of clusters + ## if the input fasta file has pre-defined classification term +diff --git a/clstr_reduce.pl b/clstr_reduce.pl +index 990f4ad..3621025 100755 +--- a/clstr_reduce.pl ++++ b/clstr_reduce.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + + $file90 = shift; +diff --git a/clstr_renumber.pl b/clstr_renumber.pl +index b542304..c66088d 100755 +--- a/clstr_renumber.pl ++++ b/clstr_renumber.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + $no = 0; + while($ll=<>){ + if ($ll =~ /^>Cluster (\d+)/) { +diff --git a/clstr_rep.pl b/clstr_rep.pl +index 0ebeb88..84b86b3 100755 +--- a/clstr_rep.pl ++++ b/clstr_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $rep = ""; + $no = 0; +diff --git a/clstr_reps_faa_rev.pl b/clstr_reps_faa_rev.pl +index 80a4a8a..3574b2b 100755 +--- a/clstr_reps_faa_rev.pl ++++ b/clstr_reps_faa_rev.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # output single fasta file + # for each cluster output at least $cutoff seqs + +diff --git a/clstr_rev.pl b/clstr_rev.pl +index d7efdcc..71134e2 100755 +--- a/clstr_rev.pl ++++ b/clstr_rev.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # if nr90 from nr100 and + # nr80 from nr90, so I have nr90.clstr and nr80.clstr + # but, in nr80.clstr, some gi numbers whose from nr100 are there +diff --git a/clstr_select.pl b/clstr_select.pl +index 1b168d9..dc70147 100755 +--- a/clstr_select.pl ++++ b/clstr_select.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #my $by = shift; + my $min; +diff --git a/clstr_select_rep.pl b/clstr_select_rep.pl +index 80c7b7e..f7c38f4 100755 +--- a/clstr_select_rep.pl ++++ b/clstr_select_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #my $by = shift; + my $min; +diff --git a/clstr_size_histogram.pl b/clstr_size_histogram.pl +index 01ecb63..b726e46 100755 +--- a/clstr_size_histogram.pl ++++ b/clstr_size_histogram.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n"; +diff --git a/clstr_size_stat.pl b/clstr_size_stat.pl +index b234b06..ecda7db 100755 +--- a/clstr_size_stat.pl ++++ b/clstr_size_stat.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_size_stat.pl clstr_file\n"; +diff --git a/clstr_sort_by.pl b/clstr_sort_by.pl +index 82e9cf8..adb12d8 100755 +--- a/clstr_sort_by.pl ++++ b/clstr_sort_by.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $sort_by_what = shift; + $sort_by_what = "no" unless $sort_by_what; +diff --git a/clstr_sort_prot_by.pl b/clstr_sort_prot_by.pl +index 64f19e2..0832b99 100755 +--- a/clstr_sort_prot_by.pl ++++ b/clstr_sort_prot_by.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $sort_by = shift; + $sort_by = "len" unless ($sort_by); +diff --git a/clstr_sql_tbl.pl b/clstr_sql_tbl.pl +index f2dba07..68bfd7d 100755 +--- a/clstr_sql_tbl.pl ++++ b/clstr_sql_tbl.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n"; +diff --git a/clstr_sql_tbl_sort.pl b/clstr_sql_tbl_sort.pl +index 67d60a8..3dfe9c4 100755 +--- a/clstr_sql_tbl_sort.pl ++++ b/clstr_sql_tbl_sort.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + if(@ARGV==0){ + print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n"; +diff --git a/make_multi_seq.pl b/make_multi_seq.pl +index 7b05636..3678654 100755 +--- a/make_multi_seq.pl ++++ b/make_multi_seq.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #note you have to use "-d 0" in the cd-hit run + #note you better to use "-g 1" in the cd-hit run +diff --git a/plot_2d.pl b/plot_2d.pl +index 418a5cf..91342ca 100755 +--- a/plot_2d.pl ++++ b/plot_2d.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + use Image::Magick; + +diff --git a/plot_len1.pl b/plot_len1.pl +index efcdfe0..e8be6e3 100755 +--- a/plot_len1.pl ++++ b/plot_len1.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + $file90 = shift; + $segs = shift; +diff --git a/psi-cd-hit/cd-hit-div.pl b/psi-cd-hit/cd-hit-div.pl +index e349394..db8d942 100755 +--- a/psi-cd-hit/cd-hit-div.pl ++++ b/psi-cd-hit/cd-hit-div.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + #not like cd-hit-div, this script do not sort input + #or throw away seq +diff --git a/psi-cd-hit/clstr_select_rep.pl b/psi-cd-hit/clstr_select_rep.pl +index b465586..63db0ce 100755 +--- a/psi-cd-hit/clstr_select_rep.pl ++++ b/psi-cd-hit/clstr_select_rep.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $by = shift; + my $min; +diff --git a/psi-cd-hit/clstr_select_seq.pl b/psi-cd-hit/clstr_select_seq.pl +index fd7bb8b..598b0e9 100755 +--- a/psi-cd-hit/clstr_select_seq.pl ++++ b/psi-cd-hit/clstr_select_seq.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my $by = shift; + my $min; +diff --git a/psi-cd-hit/fetch_fasta_by_ids.pl b/psi-cd-hit/fetch_fasta_by_ids.pl +index bfdbb26..9c17504 100755 +--- a/psi-cd-hit/fetch_fasta_by_ids.pl ++++ b/psi-cd-hit/fetch_fasta_by_ids.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my ($gi_file, $seq_file) = @ARGV; + +diff --git a/psi-cd-hit/fetch_fasta_exclude_ids.pl b/psi-cd-hit/fetch_fasta_exclude_ids.pl +index 90e237e..13d061a 100755 +--- a/psi-cd-hit/fetch_fasta_exclude_ids.pl ++++ b/psi-cd-hit/fetch_fasta_exclude_ids.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + my ($gi_file, $seq_file) = @ARGV; + +diff --git a/psi-cd-hit/psi-2d.pl b/psi-cd-hit/psi-2d.pl +index ab3f655..f3884a3 100755 +--- a/psi-cd-hit/psi-2d.pl ++++ b/psi-cd-hit/psi-2d.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + + + my $script_name = $0; +diff --git a/psi-cd-hit/psi-cd-hit-local-old.pl b/psi-cd-hit/psi-cd-hit-local-old.pl +index f5ab1b1..21fd706 100755 +--- a/psi-cd-hit/psi-cd-hit-local-old.pl ++++ b/psi-cd-hit/psi-cd-hit-local-old.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + ################################################################################ + ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org + ################################################################################ +@@ -1138,7 +1138,7 @@ sub write_remote_perl_script { + + open(REPERL, "> $remote_perl_script") || die; + print REPERL < $remote_perl_script") || die; + print REPERL <){ if (/^@/) {$i++; print ">Sample|$SAMPLE|$i ", substr($_,1); $a=<>; print $a; $a=<>; $a=<>;}}' < $SELF/R1.fq > $SELF/R1.fa & + perl -e '$i=0; while(<>){ if (/^@/) {$i++; print ">Sample|$SAMPLE|$i ", substr($_,1); $a=<>; print $a; $a=<>; $a=<>;}}' < $SELF/R2.fq > $SELF/R2.fa & +- + wait ++gzip $SELF/R1.fa & ++gzip $SELF/R2.fa & ++wait ++ + rm -f $SELF/R1.fq $SELF/R2.fq $SELF/R1-s.fq $SELF/R2-s.fq + ''' + } +@@ -61,41 +65,74 @@ rm -f $SELF/R1.fq $SELF/R2.fq $SELF/R1-s.fq $SELF/R2-s.fq + + NGS_batch_jobs['otu'] = { + 'injobs' : ['qc'], +- 'CMD_opts' : ['150', '100', '0.97', '0.0001', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1', '75'], ++ 'non_zero_files' : ['seq.99f','seq.99f.2','seq.99f-all.clstr','pool.ok'], ++ 'CMD_opts' : ['150', '100', '0.0005', '75', 'path_to_pooled_sample_dir'], + 'execution' : 'qsub_1', # where to execute + 'cores_per_cmd' : 2, # number of threads used by command below + 'no_parallel' : 1, # number of total jobs to run using command below + 'command' : ''' +-#### cluster at 100% PE +-$ENV.CD_HIT_dir/cd-hit-est -i $INJOBS.0/R1.fa -j $INJOBS.0/R2.fa -o $SELF/seq.nr -op $SELF/seq.nr.2 -sf 1 -sc 1 -P 1 -r 0 \\ ++ ++#### 1. cluster at 100% PE ++$ENV.CD_HIT_dir/cd-hit-est -i $INJOBS.0/R1.fa.gz -j $INJOBS.0/R2.fa.gz -o $SELF/seq.nr -op $SELF/seq.nr.2 -sf 1 -sc 1 -P 1 -r 0 \\ + -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 1.0 -n 10 -G 1 -b 1 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.nr.log +-#### cluster at 99% PE and SE for R1,R2 +-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -o $SELF/seq.chimeric-clstr.R1 -r 0 -cx $CMDOPTS.6 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R1.log +-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr.2 -o $SELF/seq.chimeric-clstr.R2 -r 0 -cx $CMDOPTS.6 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R2.log ++ ++#### 2. cluster at 99% PE + $ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -j $SELF/seq.nr.2 -o $SELF/seq.99 -op $SELF/seq.99.2 -P 1 -r 0 \\ + -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.99 -n 10 -G 1 -b 1 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.99.log +-$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-chimeric-and-small.pl -c $CMDOPTS.3 -k $SELF/seq.nr.clstr \\ ++ ++#### 3. cluster at 99% SE for R1, R2 ++$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr -o $SELF/seq.chimeric-clstr.R1 -r 0 -cx $CMDOPTS.3 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R1.log ++$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.nr.2 -o $SELF/seq.chimeric-clstr.R2 -r 0 -cx $CMDOPTS.3 -c 0.99 -n 10 -G 0 -b 1 -A 50 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.chimeric-clstr.R2.log ++rm -f $SELF/seq.chimeric-clstr.R1 $SELF/seq.chimeric-clstr.R1.log \\ ++ $SELF/seq.chimeric-clstr.R2 $SELF/seq.chimeric-clstr.R2.log ++ ++#### 4. 5. filter chimeric sequences and sequences in small clusters ++$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-chimeric-and-small.pl -c $CMDOPTS.2 -k $SELF/seq.nr.clstr \\ + -i $SELF/seq.chimeric-clstr.R1.clstr -j $SELF/seq.chimeric-clstr.R2.clstr \\ + -a $SELF/seq.99.clstr -f $SELF/seq.99 -g $SELF/seq.99.2 -o $SELF/seq.99f + $ENV.CD_HIT_dir/clstr_rev.pl $SELF/seq.nr.clstr $SELF/seq.99f.clstr > $SELF/seq.99f-all.clstr +-$ENV.CD_HIT_dir/cd-hit-est -i $SELF/seq.99f -j $SELF/seq.99f.2 -o $SELF/seq.97 -op $SELF/seq.97.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.97.log +-$ENV.CD_HIT_dir/cd-hit-est-2d -i $SELF/seq.97 -j $SELF/seq.97.2 -i2 $CMDOPTS.4 -j2 $CMDOPTS.5 -o $SELF/seq.97.ref -op $SELF/seq.97.ref.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > $SELF/seq.97.ref.log +-$ENV.CD_HIT_dir/clstr_rev.pl $SELF/seq.99f-all.clstr $SELF/seq.97.clstr > $SELF/seq.97-all.clstr +-$ENV.CD_HIT_dir/usecases/Miseq-16S/filter-nontop-ref.pl < $SELF/seq.97.ref.clstr > $SELF/seq.97.reftop.clstr +-$ENV.CD_HIT_dir/clstr_merge.pl $SELF/seq.97-all.clstr $SELF/seq.97.reftop.clstr > $SELF/OTU.clstr +- +-rm -f $SELF/seq.chimeric-clstr.R1 $SELF/seq.chimeric-clstr.R1.log $SELF/seq.chimeric-clstr.R2 $SELF/seq.chimeric-clstr.R2.log +-rm -f $SELF/seq.97.ref $SELF/seq.97.ref.2 $SELF/seq.97.ref.log + mv $SELF/seq.99f.log $SELF/chimeric-small-clusters-list.txt + ++ ++#### ++if [ ! -e "$CMDOPTS.4" ]; then ++ mkdir -p $CMDOPTS.4 ++fi ++ ++i="0" ++while [ 1 ]; do ++ ++ if [ -e "$CMDOPTS.4/lock" ]; then ++ echo "wait $CMDOPTS.4/lock" ++ sleep 5 ++ else ++ date > $CMDOPTS.4/lock ++ ++ cat $SELF/seq.99f >> $CMDOPTS.4/seq.99f ++ cat $SELF/seq.99f.2 >> $CMDOPTS.4/seq.99f.2 ++ cat $SELF/seq.99f-all.clstr >> $CMDOPTS.4/seq.99f-all.clstr ++ cat $SELF/chimeric-small-clusters-list.txt >> $CMDOPTS.4/chimeric-small-clusters-list.txt ++ date > $SELF/pool.ok ++ sleep 1 ++ ++ rm -f $CMDOPTS.4/lock ++ break ++ fi ++ ++ i=$[$i+1] ++ if [ "$i" -gt "50" ]; then ++ echo "wait $CMDOPTS.4/lock for too long" ++ break ++ fi ++done ++ + ''' + } + + + NGS_batch_jobs['otu-pooled'] = { +- 'CMD_opts' : ['150', '100', '0.97', '0.0001', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1', '75'], ++ 'CMD_opts' : ['150', '100', '0.97', 'path_to_spliced_ref_db-R1', 'path_to_spliced_ref_db-R1'], ++ 'non_zero_files' : ['OTU.txt'], + 'execution' : 'qsub_1', # where to execute + 'cores_per_cmd' : 2, # number of threads used by command below + 'no_parallel' : 1, # number of total jobs to run using command below +@@ -103,9 +140,9 @@ NGS_batch_jobs['otu-pooled'] = { + #### before running + #### concat seq.99f seq.99f.2 seq.99f-all.clstr chimeric-small-clusters-list.txt + $ENV.CD_HIT_dir/cd-hit-est -i seq.99f -j seq.99f.2 -o seq.97 -op seq.97.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.log +-$ENV.CD_HIT_dir/cd-hit-est-2d -i seq.97 -j seq.97.2 -i2 $CMDOPTS.4 -j2 $CMDOPTS.5 -o seq.97.ref -op seq.97.ref.2 -P 1 -r 0 \\ +- -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c 0.97 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.ref.log ++ -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c $CMDOPTS.2 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.log ++$ENV.CD_HIT_dir/cd-hit-est-2d -i seq.97 -j seq.97.2 -i2 $CMDOPTS.3 -j2 $CMDOPTS.4 -o seq.97.ref -op seq.97.ref.2 -P 1 -r 0 \\ ++ -cx $CMDOPTS.0 -cy $CMDOPTS.1 -c $CMDOPTS.2 -n 10 -G 1 -b 10 -T 1 -M 8000 -d 0 -p 1 > seq.97.ref.log + $ENV.CD_HIT_dir/clstr_rev.pl seq.99f-all.clstr seq.97.clstr > seq.97-all.clstr + $ENV.CD_HIT_dir/usecases/Miseq-16S/filter-nontop-ref.pl < seq.97.ref.clstr > seq.97.reftop.clstr + $ENV.CD_HIT_dir/clstr_merge.pl seq.97-all.clstr seq.97.reftop.clstr > OTU.clstr +diff --git a/usecases/Miseq-16S/NG-Omics-WF.pl b/usecases/Miseq-16S/NG-Omics-WF.pl +index 2f46255..195583e 100755 +--- a/usecases/Miseq-16S/NG-Omics-WF.pl ++++ b/usecases/Miseq-16S/NG-Omics-WF.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl ++#!/usr/bin/env perl + # =============================== NG-Omics-WF ================================== + # _ _ _____ ____ _ __ ________ + # | \ | |/ ____| / __ \ (_) \ \ / / ____| +diff --git a/usecases/Miseq-16S/OTU_2_taxon_table.pl b/usecases/Miseq-16S/OTU_2_taxon_table.pl +new file mode 100755 +index 0000000..86561af +--- /dev/null ++++ b/usecases/Miseq-16S/OTU_2_taxon_table.pl +@@ -0,0 +1,158 @@ ++#!/usr/bin/env perl ++## =========================== NGS tools ========================================== ++## NGS tools for metagenomic sequence analysis ++## May also be used for other type NGS data analysis ++## ++## Weizhong Li, UCSD ++## liwz@sdsc.edu ++## http://weizhongli-lab.org/ ++## ================================================================================ ++ ++use Getopt::Std; ++getopts("i:o:a:t:r:N:c:P:",\%opts); ++die usage() unless ($opts{o} and $opts{i} and $opts{t}); ++ ++ ++my $otu_table = $opts{i}; ### e.g. OTU-short.txt ++my $taxon_file = $opts{t}; ### e.g. OTU-feature.txt ++my $output = $opts{o}; ++ ++my ($i, $j, $k, $ll, $cmd); ++ ++my @samples = (); ++my @otus = (); ++my %otu_mat = (); ++ ++my $fh; ++if ($otu_table eq "-") { $fh = "STDIN";} ++else { ++ open(TMP, $otu_table) || die "can not open $otu_table"; ++ $fh = "TMP"; ++} ++ ++$ll = <$fh>; chop($ll); ++my ($t1, @lls) = split(/\t/, $ll); ++@samples = @lls; ++my $num_samples = $#samples+1; ++ ++while($ll=<$fh>){ ++ next if ($ll =~ /^#/); ++ next unless ($ll =~ /^otu/i); ++ chop($ll); ++ my ($otu, @v) = split(/\t/, $ll); ++ push(@otus, $otu); ++ for ($i=0; $i<$num_samples; $i++) { ++ $otu_mat{$otu}{$samples[$i]} = $v[$i]; ++ } ++} ++ ++open(TMP, $taxon_file) || die "can not open $taxon_file"; ++my %taxon_info = (); ++while($ll=) { ++ chop($ll); ++ next if ($ll =~ /^#/); ++ my ($otu, $taxon, $c) = split(/\t/, $ll); ++ # next unless ($taxon =~ /__/); #### skip unknown OTUs ++ ++#OTUID taxonomy confidence ++#OTU1 Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__ 1.0 ++#OTU2 Root;k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16;g__;s__ 1.0 ++#OTU3 Root;k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Flexispira;s__rappini 1.0 ++#OTU4 Root;k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio;s__C21_c20 1.0 ++ ++ my $k = "unclassified"; ++ my $p = "unclassified"; ++ my $c = "unclassified"; ++ my $o = "unclassified"; ++ my $f = "unclassified"; ++ my $g = "unclassified"; ++ my $s = "unclassified"; ++ ++ $j = $taxon; ++ if ($j =~ /^k__([^;]+)/) {$k = $1;} ++ if ($j =~ /;k__([^;]+)/) {$k = $1;} ++ if ($j =~ /;p__([^;]+)/) {$p = $1;} ++ if ($j =~ /;c__([^;]+)/) {$c = $1;} ++ if ($j =~ /;o__([^;]+)/) {$o = $1;} ++ if ($j =~ /;f__([^;]+)/) {$f = $1;} ++ if ($j =~ /;g__([^;]+)/) {$g = $1;} ++ if ($j =~ /;s__([^;]+)/) {$s = $1;} ++ ++ if ($j =~ /^D_0__([^;]+)/) {$k = $1;} ++ if ($j =~ /;D_0__([^;]+)/) {$k = $1;} ++ if ($j =~ /;D_1__([^;]+)/) {$p = $1;} ++ if ($j =~ /;D_2__([^;]+)/) {$c = $1;} ++ if ($j =~ /;D_3__([^;]+)/) {$o = $1;} ++ if ($j =~ /;D_4__([^;]+)/) {$f = $1;} ++ if ($j =~ /;D_5__([^;]+)/) {$g = $1;} ++ if ($j =~ /;D_6__([^;]+)/) {$s = $1;} ++ ++ if (($g ne "unclassified") and ($s ne "unclassified")) { ++ if ( substr($s, 0, length($g)) ne $g) { #### if species name doesn't contain genus name, add ++ $s = "$g $s"; ++ } ++ } ++ $taxon_info{$otu} = [$k,$p,$c,$o,$f,$g,$s]; ++ ++} ++close(TMP); ++ ++my @ranks = qw/kingdom phylum class order family genus species/; ++my %rank_col = qw/kingdom 0 phylum 1 class 2 order 3 family 4 genus 5 species 6/; ++foreach $rank (@ranks) { ++ next if ($rank eq "kingdom"); ++ ++ my $c = $rank_col{$rank}; ++ my $out = "$output.$rank.txt"; ++ open(OUT, "> $out") || die "can not write to $out"; ++ #### print table header ++ print OUT "#", join("\t", @ranks[0..$c]); ++ print OUT "\t", join("\t", @samples), "\n"; ++ ++ my %rank_ti_info = (); ++ my %rank_mat = (); ++ my %ti_sum = (); ++ foreach $otu (@otus) { ++ my @ann = @{$taxon_info{$otu}}; ++ my $ti = join("|", @ann[0 .. $c] ); ++ ++ if (not defined($rank_ti_info{$ti})) { ++ $rank_ti_info{$ti} = [ @ann[0 .. $c] ]; ++ } ++ foreach $sample (@samples) { ++ $rank_mat{$ti}{$sample} += $otu_mat{$otu}{$sample}; ++ $ti_sum{$ti} += $otu_mat{$otu}{$sample}; ++ } ++ } ++ my @tis = keys %rank_mat; ++ @tis = sort {$ti_sum{$b} <=> $ti_sum{$a} } @tis; ++ ++ foreach $ti (@tis) { ++ print OUT join("\t", @{ $rank_ti_info{$ti} } ); ++ foreach $sample (@samples) { ++ print OUT "\t", $rank_mat{$ti}{$sample}; ++ } ++ print OUT "\n"; ++ } ++ close(OUT); ++} ++ ++ ++sub usage { ++<){ + $count_s{$sample_id}++; + } + else { ++ $id =~ s/^([^\|]+)\|//; ++ $id =~ s/;\./;/g; ++ $id = "Root;$id"; ++ $id =~ s/;D_0__/;k__/; ++ $id =~ s/;D_1__/;p__/; ++ $id =~ s/;D_2__/;c__/; ++ $id =~ s/;D_3__/;o__/; ++ $id =~ s/;D_4__/;f__/; ++ $id =~ s/;D_5__/;g__/; ++ $id =~ s/;D_6__/;s__/; + $OTU_2_ann{$OTU} = $id; +- $tree_flag = 1 if ($id =~ /\|k__Bacteria;.p__/); ++ $tree_flag = 1 if ($id =~ /;k__Bacteria/); + } + } + else { +@@ -45,23 +66,34 @@ close(TMP); + my @sample_ids = sort keys %sample_id; + + open(OUT1, "> $output") || die "can not write $output"; +-print OUT1 "OTU"; ++open(OUT2, "> $output_short") || die "can not write $output_short"; ++open(OUT3, "> $output_feature") || die "can not write $output_feature"; ++ ++print OUT1 "#OTUID"; ++print OUT2 "#OTUID"; ++print OUT3 "#OTUID"; + foreach $sample_id (@sample_ids){ + print OUT1 "\t$sample_id"; ++ print OUT2 "\t$sample_id"; + } + if ($tree_flag) { + print OUT1 "\t", join("\t", qw/Kingdom Phylum Class Order Family Genus Species/); + } + #print OUT1 "\tTotal\n"; + print OUT1 "\tAnnotation\n"; ++print OUT2 "\n"; ++print OUT3 "\ttaxonomy\tconfidence\n"; + + for ($i=1; $i<=$OTU; $i++){ +- $ann = "None"; ++ $ann = ""; + if ($OTU_2_ann{$i}) { $ann = $OTU_2_ann{$i}; } + print OUT1 "OTU$i"; ++ print OUT2 "OTU$i"; ++ print OUT3 "OTU$i"; + foreach $sample_id (@sample_ids){ + $k = $count{$i}{$sample_id}? $count{$i}{$sample_id} : 0; + print OUT1 "\t$k"; ++ print OUT2 "\t$k"; + } + if ($tree_flag) { + my ($tax_k, $tax_p, $tax_c, $tax_o, $tax_f, $tax_g, $tax_s); +@@ -76,7 +108,37 @@ for ($i=1; $i<=$OTU; $i++){ + } + #print OUT1 "\t$count_t{$i}"; + print OUT1 "\t$ann\n"; ++ print OUT2 "\n"; ++ print OUT3 "\t$ann\t1.0\n"; + } + close(OUT1); ++close(OUT2); ++close(OUT3); ++ ++open(OUT, ">$output_meta") || die "can not write to $output_meta"; ++print OUT "#SampleID\tGroup\n"; ++foreach $sample_id (@sample_ids){ ++ print OUT "$sample_id\tnogroup\n"; ++} ++close(OUT); + ++if (-e $biom_exe) { ++ $cmd = `$biom_exe convert -i $output_short -o $output_biom --to-hdf5 --observation-metadata-fp $output_feature --sample-metadata-fp $output_meta`; ++} ++ ++sub usage { ++<){ ++ chop($ll); ++ my ($id, $txt) = split(/\s+/, $ll, 2); ++ $txt =~ s/ /./g; ++ $id_2_ann{$id} = $txt; ++} ++close(TMP); ++ ++my %id_2_seq = (); ++my $id = ""; ++open(TMP, $fasta) || die "can not open $fasta"; ++while($ll=){ ++ if ($ll =~ /^>(\S+)/) { ++ chop($ll); ++ $id = $1; ++ $ann = $id_2_ann{$id}; ++ $id = "$id|$ann" if ($ann); ++ } ++ else { ++ $id_2_seq{$id} .= $ll; ++ } ++} ++ ++close(TMP); ++ ++my @ids = keys %id_2_seq; ++ @ids = sort {length($b) <=> length($a) } @ids; ++ ++open(OUT, "> $output") || die "can not write to $output"; ++foreach $id (@ids) { ++ print OUT ">$id\n$id_2_seq{$id}"; ++} ++close(OUT); ++ ++ ++ ++sub usage { ++< /dev/null about: - home: https://github.com/weizhongli/cdhit - license: GPLv2 - summary: Clusters and compares protein or nucleotide sequences + home: "https://github.com/weizhongli/cdhit" + license: "GPL-2.0-or-later" + license_family: GPL + license_file: "license.txt" + summary: "Clusters and compares protein or nucleotide sequences." + dev_url: "https://github.com/weizhongli/cdhit" + doc_url: "https://github.com/weizhongli/cdhit/wiki" extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 + - osx-arm64 + identifiers: + - doi:10.1093/bioinformatics/17.3.282 + - doi:10.1093/bioinformatics/18.1.77 + - biotools:cd-hit + - usegalaxy-eu:cd_hit diff --git a/recipes/cellprofiler/meta.yaml b/recipes/cellprofiler/meta.yaml index 813f6bbada87d..e0cde02fab3b5 100644 --- a/recipes/cellprofiler/meta.yaml +++ b/recipes/cellprofiler/meta.yaml @@ -1,5 +1,5 @@ {% set name = "CellProfiler" %} -{% set version = "4.2.7" %} +{% set version = "4.2.8" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/CellProfiler/{{ name }}/archive/v{{ version }}.tar.gz - sha256: "8bc0819f1e2c215756e7eb5b7f0078949760d707397930eddf002b8bdd452ed3" + sha256: "c1352e703ca36af63b6069fda9a0de3b54980ed0d2b7d45d08c84fbeeded03fd" build: number: 0 @@ -23,6 +23,7 @@ requirements: - python >=3.8 - pip - pytest + - setuptools run: - python >=3.8 - boto3 >=1.12.28 diff --git a/recipes/centrifuger/meta.yaml b/recipes/centrifuger/meta.yaml index dccd1d4dbe4d6..196d36ed4e995 100644 --- a/recipes/centrifuger/meta.yaml +++ b/recipes/centrifuger/meta.yaml @@ -1,18 +1,18 @@ {% set name = "centrifuger" %} -{% set version = "1.0.4" %} +{% set version = "1.0.5" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} source: url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 5261abcfb3b88126000ae7708702d07704a0ee19d6f54f9f89f0d2e195e24d1d + sha256: 1de388229d3ee6a65a58308b5521bef6cbfcdf92628064a39d6b70c7523d68de requirements: build: diff --git a/recipes/cooltools/meta.yaml b/recipes/cooltools/meta.yaml index 334ffd72b4937..cb8b5698bca2c 100644 --- a/recipes/cooltools/meta.yaml +++ b/recipes/cooltools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cooltools" %} -{% set version = "0.7.0" %} +{% set version = "0.7.1" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8b26d4857cc76b2dd3d1097b85f828cf6d5f1cf85b0cfd4b67a310e33e7ece1c + sha256: 1f12494add7b1271b71e418d10d060e1dac906a021fc2bd691e91f5599010051 build: - number: 2 + number: 0 entry_points: - cooltools = cooltools.cli:cli script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" diff --git a/recipes/coptr/meta.yaml b/recipes/coptr/meta.yaml index d60f860e17a92..cbc6774b24785 100644 --- a/recipes/coptr/meta.yaml +++ b/recipes/coptr/meta.yaml @@ -14,19 +14,19 @@ build: - coptr = coptr.cli:cli noarch: python script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir - number: 1 + number: 3 run_exports: - {{ pin_subpackage("coptr", max_pin="x") }} requirements: host: - - python >=3.7 + - python >=3.7,<=3.8 - setuptools - pip run: - bowtie2 >=2.4.1 - - python >=3.7 - - numpy >=1.19.1 + - python >=3.7,<=3.8 + - numpy >=1.19.1,<=1.24.4 - pysam >=0.16.0.1 - scipy >=1.5.2,<2.0.0 - matplotlib-base >=3.3.2 diff --git a/recipes/cuttlefish/build.sh b/recipes/cuttlefish/build.sh index 8cc1be2aece0d..d232e1650bf24 100644 --- a/recipes/cuttlefish/build.sh +++ b/recipes/cuttlefish/build.sh @@ -1,24 +1,25 @@ #!/bin/bash -mkdir build -cd build +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -fcommon -I${PREFIX}/include" -unamestr=`uname` - -if [ "$unamestr" == 'Darwin' ]; -then - export MACOSX_DEPLOYMENT_TARGET=10.15 - export CFLAGS="${CFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY" - export CXXFLAGS="${CXXFLAGS} -fcommon -D_LIBCPP_DISABLE_AVAILABILITY" -else - # It's dumb and absurd that the KMC build can't find the bzip2 header - export C_INCLUDE_PATH="$PREFIX/include" - export CPLUS_INCLUDE_PATH="$PREFIX/include" +if [[ `uname` == 'Darwin' ]]; then + export MACOSX_DEPLOYMENT_TARGET=10.11 + export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY" + export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER" +else + # It's dumb and absurd that the KMC build can't find the bzip2 header + export C_INCLUDE_PATH="$PREFIX/include" + export CPLUS_INCLUDE_PATH="$PREFIX/include" + export CONFIG_ARGS="" fi -cmake \ - -DINSTANCE_COUNT=64 \ - -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ - -DCONDA_BUILD=ON \ - .. -make install +cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_CXX_COMPILER="${CXX}" \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DINSTANCE_COUNT=64 \ + -DCMAKE_INSTALL_PREFIX="${PREFIX}" \ + "${CONFIG_ARGS}" +cmake --build build/ --target install -j "${CPU_COUNT}" -v diff --git a/recipes/cuttlefish/build_failure.osx-64.yaml b/recipes/cuttlefish/build_failure.osx-64.yaml deleted file mode 100644 index 5478b7be1ea8e..0000000000000 --- a/recipes/cuttlefish/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 88d29dc5a3f896af86f91bbb69279e4bd0a02dfb550bb0080c44599f527cd38d # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - kmc_core/kb_sorter.h:231:3: note: in instantiation of member function 'CKmerBinSorter<2>::Compact' requested here - Compact(); - ^ - kmc_core/kb_sorter.h:1321:7: note: in instantiation of member function 'CKmerBinSorter<2>::ProcessBins' requested here - kbs->ProcessBins(); - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: (skipping 22 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) - { return static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); } - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<4>::ProcessStage2' requested here - return app_1->ProcessStage2(stage2Params); - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<5>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<6>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<7>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:424:16: note: in instantiation of member function 'KMC::CApplication<8>::ProcessStage2' requested here - return app->ProcessStage2(stage2Params); - ^ - In file included from kmc_core/kmc_runner.cpp:12: - In file included from kmc_core/kmc.h:30: - In file included from kmc_core/kb_sorter.h:33: - kmc_core/kxmer_set.h:282:13: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] - data.push(move(sub_array_desc_copy)); - ^ - std:: - kmc_core/kxmer_set.h:304:10: warning: unqualified call to 'std::move' [-Wunqualified-std-cast-call] - desc = move(data.front()); - ^ - std:: - kmc_core/kxmer_set.h:572:35: note: in instantiation of member function 'CSubArrayDescGenerator<2>::GetNext' requested here - while (sub_array_desc_generator.GetNext(desc, out_start)) - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of member function 'CKXmerMerger<2>::operator()' requested here - { return static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); } - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of function template specialization 'std::reference_wrapper>::operator()<>' requested here - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/bind.h:295:27: note: in instantiation of function template specialization 'std::__apply_functor>, std::tuple<>, std::tuple<>>' requested here - return _VSTD::__apply_functor(__f_, __bound_args_, __indices(), - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/invoke.h:394:23: note: in instantiation of function template specialization 'std::__bind>>::operator()<>' requested here - { return static_cast<_Fp&&>(__f)(static_cast<_Args&&>(__args)...); } - ^ - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__functional/function.h:185:26: note: (skipping 40 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) - return _Invoker::__call(__f_.first(), - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<4>::ProcessStage2' requested here - return app_1->ProcessStage2(stage2Params); - ^ - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<5>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<6>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:65:19: note: in instantiation of member function 'KMC::CApplication<7>::ProcessStage2' requested here - kmc_core/kmc_runner.cpp:424:16: note: in instantiation of member function 'KMC::CApplication<8>::ProcessStage2' requested here - return app->ProcessStage2(stage2Params); - ^ - In file included from kmc_core/kmc_runner.cpp:12: - In file included from kmc_core/kmc.h:15: - In file included from kmc_core/params.h:21: - kmc_core/libs/ntHash/ntHashWrapper.h:110:7: warning: private field 'convert' is not used [-Wunused-private-field] - char convert[256] = { - ^ - 127 warnings generated. - [ 12%] Performing install step for 'prj_kmc' - [ 14%] Completed 'prj_kmc' - [ 14%] Built target prj_kmc - [ 16%] Building CXX object src/CMakeFiles/cfcore_static.dir/kmc_api/kmc_file.cpp.o - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/src/kmc_api/kmc_file.cpp:12: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/include/kmc_api/stdafx.h:3: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/iostream:43: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/ios:221: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__locale:18: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/mutex:191: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/shared_ptr.h:22: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/allocation_guard.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/allocator_traits.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/__memory/construct_at.h:23: - /opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/_build_env/bin/../include/c/v1/new:355:14: error: no member named 'aligned_alloc' in the global namespace - return ::aligned_alloc(__alignment, __size > __rounded_size ? __size : __rounded_size); - ~~^ - 1 error generated. - make[2]: *** [src/CMakeFiles/cfcore_static.dir/build.make:76: src/CMakeFiles/cfcore_static.dir/kmc_api/kmc_file.cpp.o] Error 1 - make[1]: *** [CMakeFiles/Makefile2:130: src/CMakeFiles/cfcore_static.dir/all] Error 2 - make: *** [Makefile:136: all] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/cuttlefish_1685354286097/work/conda_build.sh']' returned non-zero exit status 2. -# Last 100 lines of the build log. diff --git a/recipes/cuttlefish/meta.yaml b/recipes/cuttlefish/meta.yaml index d76c858dd233d..f2cef96e5af21 100644 --- a/recipes/cuttlefish/meta.yaml +++ b/recipes/cuttlefish/meta.yaml @@ -6,7 +6,9 @@ package: version: {{ version }} build: - number: 2 + number: 3 + run_exports: + - {{ pin_subpackage('cuttlefish', max_pin="x") }} source: url: https://github.com/COMBINE-lab/cuttlefish/archive/refs/tags/v{{ version }}.tar.gz @@ -14,20 +16,14 @@ source: requirements: build: - - autoconf - cmake >=3.14.0 - make - {{ compiler('cxx') }} - {{ compiler('c') }} - - zlib - - bzip2 host: - jemalloc >=5.1.0 - zlib - bzip2 - run: - - bzip2 - - zlib test: commands: @@ -36,17 +32,21 @@ test: - cuttlefish version about: - home: https://github.com/COMBINE-lab/cuttlefish - license: BSD-3-Clause + home: "https://github.com/COMBINE-lab/cuttlefish" + license: "BSD-3-Clause" + license_family: BSD license_file: LICENSE - summary: Construction of the compacted de Bruijn graph efficiently - dev_url: https://github.com/COMBINE-lab/cuttlefish - doc_url: https://github.com/COMBINE-lab/cuttlefish#readme + summary: "Construction of the compacted de Bruijn graph efficiently." + dev_url: "https://github.com/COMBINE-lab/cuttlefish" + doc_url: "https://github.com/COMBINE-lab/cuttlefish/blob/v{{ version }}/README.md" extra: + additional-platforms: + - osx-arm64 recipe-maintainers: - jamshed - rob-p identifiers: - doi:10.1093/bioinformatics/btab309 - doi:10.1186/s13059-022-02743-6 + - biotools:cuttlefish diff --git a/recipes/deepchopper-cli/build.sh b/recipes/deepchopper-cli/build.sh index 191874d4ab76a..406a030b71a26 100644 --- a/recipes/deepchopper-cli/build.sh +++ b/recipes/deepchopper-cli/build.sh @@ -4,16 +4,12 @@ # -x = print every executed command set -ex -# if [ `uname` == Darwin ]; then -# export HOME=`mktemp -d` -# fi - curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y export PATH="$HOME/.cargo/bin:$PATH" cd py_cli -maturin build --interpreter python --release -b bin --out dist +maturin build --interpreter "${PYTHON}" --release --strip -b bin --out dist -$PYTHON -m pip install dist/*.whl --no-deps --ignore-installed -vv +$PYTHON -m pip install dist/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/deepchopper-cli/meta.yaml b/recipes/deepchopper-cli/meta.yaml index d14e1b8fb0005..45fceb4596974 100644 --- a/recipes/deepchopper-cli/meta.yaml +++ b/recipes/deepchopper-cli/meta.yaml @@ -1,6 +1,6 @@ {% set name = "deepchopper-cli" %} -{% set version = "1.2.5" %} -{% set sha256 = "fc5ceaf204f82eeae1b82488ee44d020c66b0df13d27a86658ed86a7b1774dbb" %} +{% set version = "1.2.6" %} +{% set sha256 = "2ea385c3bb6e95f2d76627c2c6a859cfdab7f3402bd4589b1e787d301df1fbd1" %} package: name: {{ name|lower }} diff --git a/recipes/deepchopper/build.sh b/recipes/deepchopper/build.sh index ba2ee9778318d..57474c5448ba7 100644 --- a/recipes/deepchopper/build.sh +++ b/recipes/deepchopper/build.sh @@ -4,17 +4,10 @@ # -x = print every executed command set -ex -# if [ `uname` == Darwin ]; then -# export HOME=`mktemp -d` -# fi - curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain nightly --profile=minimal -y export PATH="$HOME/.cargo/bin:$PATH" -# export CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER="$CC" -# export CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER="$CC" - -maturin build --interpreter python --release +maturin build --interpreter "${PYTHON}" --release --strip -$PYTHON -m pip install target/wheels/*.whl --no-deps --ignore-installed -vv +$PYTHON -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/deepchopper/meta.yaml b/recipes/deepchopper/meta.yaml index 6a0403762b1d1..a94a5edd37044 100644 --- a/recipes/deepchopper/meta.yaml +++ b/recipes/deepchopper/meta.yaml @@ -1,6 +1,6 @@ {% set name = "deepchopper" %} -{% set version = "1.2.5" %} -{% set sha256 = "77a62b80b523add11259a298d5401592ff04fa88c3108a632fd0a9c8a73faa8b" %} +{% set version = "1.2.6" %} +{% set sha256 = "f264d1d451a9ad28073af0c2be95f177b71c39fa63a726408592bf412f56e4fe" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 skip: True # [py < 310] run_exports: - {{ pin_subpackage("deepchopper", max_pin="x") }} diff --git a/recipes/dnaio/meta.yaml b/recipes/dnaio/meta.yaml index f3d95856ef974..8d8264f4816ff 100644 --- a/recipes/dnaio/meta.yaml +++ b/recipes/dnaio/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.2.2" %} +{% set version = "1.2.3" %} package: name: dnaio version: {{ version }} source: - url: https://files.pythonhosted.org/packages/1e/69/b11040d6cb619f2c879904dfd5f703c15d5ed05d20afc556318de9bc476b/dnaio-1.2.2.tar.gz - sha256: 55e1c8e5b86056ce3bb3a3eff643ebc9910a5d6d0d5c10a27eb4d5b6525117d5 + url: https://files.pythonhosted.org/packages/ca/23/1afaeadecfe4712769db4b609ca4aeb4246f6a47a9ab39801cb6a5aa8c2e/dnaio-1.2.3.tar.gz + sha256: aad456d9f6272339958b2c5af32fd64d77a50aca12e394e7a143b4129d49b0b9 build: number: 0 @@ -20,11 +20,11 @@ requirements: - {{ compiler('c') }} host: - pip - - python + - python >=3.9 - cython - setuptools-scm run: - - python + - python >=3.9 - xopen >=1.4.0 test: diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml index b26c1ef097798..68c313634959b 100644 --- a/recipes/dxpy/meta.yaml +++ b/recipes/dxpy/meta.yaml @@ -1,5 +1,5 @@ {% set name = "dxpy" %} -{% set version = "0.384.0" %} +{% set version = "0.385.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 17e29e9f58843c2639d53ea02b0dfd5c9940ad4ff20ab9e4df895a664f07e392 + sha256: 6e0d06e9704e9845967caaf301e918496056ad58e15bd610fb02c3c4d775adcf build: number: 0 diff --git a/recipes/emu-pca/build_failure.osx-64.yaml b/recipes/emu-pca/build_failure.osx-64.yaml deleted file mode 100644 index faf6c61b044ce..0000000000000 --- a/recipes/emu-pca/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c8fdd7d1be49e7c2e5e03c78e8ef8e5da084a2de40931b17429baec27d330480 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ERROR: Failed building wheel for emu - ERROR: Could not build wheels for emu, which is required to install pyproject.toml-based projects - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_build_env - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work/conda_build.sh']' returned non-zero exit status 1. - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/emu-pca-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/emu-pca-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-pcf71fuv - Initialized build tracking at /private/tmp/pip-build-tracker-pcf71fuv - Created build tracker: /private/tmp/pip-build-tracker-pcf71fuv - Entered build tracker: /private/tmp/pip-build-tracker-pcf71fuv - Created temporary directory: /private/tmp/pip-install-_4p1fpa8 - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-pg6d97ox - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-pcf71fuv' - Created temporary directory: /private/tmp/pip-modern-metadata-x9ykve7d - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'done' - Source in $SRC_DIR has version 1.0, which satisfies requirement emu==1.0 from file://$SRC_DIR - Removed emu==1.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-pcf71fuv' - Created temporary directory: /private/tmp/pip-unpack-ylygux9m - Building wheels for collected packages: emu - Created temporary directory: /private/tmp/pip-wheel-f2hnm5l2 - Destination directory: /private/tmp/pip-wheel-f2hnm5l2 - Building wheel for emu (pyproject.toml): started - Building wheel for emu (pyproject.toml): finished with status 'error' - Failed to build emu - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for emu, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-pcf71fuv' -# Last 100 lines of the build log. diff --git a/recipes/emu-pca/meta.yaml b/recipes/emu-pca/meta.yaml index 3606b1fe2ba7c..f299b78443ca6 100644 --- a/recipes/emu-pca/meta.yaml +++ b/recipes/emu-pca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "emu-pca" %} -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,15 @@ package: source: url: 'https://github.com/Rosemeis/emu/archive/refs/tags/v{{ version }}.tar.gz' - md5: b79e9a2f72b8b83361a5542edc1c4ca7 + sha256: a309849df3cbd2255718ba27d413b931b835ed869a67a93cd20320d1a04d31fb build: - number: 1 + number: 0 + skip: True # [py < 310] script: - - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + - "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" + entry_points: + - emu=emu.main:main run_exports: {{ pin_subpackage('emu-pca', max_pin="x") }} @@ -37,4 +40,3 @@ about: license_file: LICENSE summary: EM-PCA for Ultra-low Coverage Sequencing Data. dev_url: https://github.com/Rosemeis/emu - diff --git a/recipes/ensembl-utils/meta.yaml b/recipes/ensembl-utils/meta.yaml index 77bbd0f6413b6..a0579103ab9f5 100644 --- a/recipes/ensembl-utils/meta.yaml +++ b/recipes/ensembl-utils/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ensembl-utils" %} -{% set version = "0.5.1" %} +{% set version = "0.6.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ensembl_utils-{{ version }}.tar.gz - sha256: 613d0f9584993aaacab42379b57b0ccbeac9f9269a99c186dddf84d396bc3c86 + sha256: ee2841af4da1b7f10d2fa88ab844f72dad17042de473759971f4ec1d870a0506 build: entry_points: diff --git a/recipes/evofr/meta.yaml b/recipes/evofr/meta.yaml index fb083c92d9933..a378a5c246003 100644 --- a/recipes/evofr/meta.yaml +++ b/recipes/evofr/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.23" %} +{% set version = "0.1.25" %} package: name: evofr @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz - sha256: ac159419119c000e403b5801d8b6dfef215bcbeca6f30f3bf13b66b90b64ad17 + sha256: 7360736349cad3a665acc80f4e6d3c4fe205a991dae2e35ab86d56b66214bf30 build: number: 0 diff --git a/recipes/fastp/meta.yaml b/recipes/fastp/meta.yaml index 148491c023d63..1cbcc0d55e8d7 100644 --- a/recipes/fastp/meta.yaml +++ b/recipes/fastp/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.23.4" %} +{% set version="0.24.0" %} package: name: fastp @@ -6,10 +6,10 @@ package: source: url: https://github.com/OpenGene/fastp/archive/v{{ version }}.tar.gz - sha256: 4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5 + sha256: 42445973c57be9209c753027e99781261c69381013813c576ad447e413ff3d04 build: - number: 5 + number: 0 run_exports: - {{ pin_subpackage("fastp", max_pin="x.x") }} diff --git a/recipes/gadma/meta.yaml b/recipes/gadma/meta.yaml index e993392fac055..57ee11d2b03b5 100644 --- a/recipes/gadma/meta.yaml +++ b/recipes/gadma/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gadma" %} -{% set version = "2.0.0" %} +{% set version = "2.0.2" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 1e891b87749261ce9c1866fd3e0ac389306096e3b940eb364101448efeca4cfd + sha256: f7b610d0d347e97afb30e6b5f9a814c19e479203838de31aa2e44f7427073db5 build: number: 0 @@ -19,27 +19,31 @@ build: - gadma-get_confidence_intervals = gadma.get_confidence_intervals:main - gadma-get_confidence_intervals_for_ld = gadma.get_confidence_intervals_for_ld:main - gadma-precompute_ld_data = gadma.precompute_ld_data:main - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: - {{ pin_subpackage('gadma', max_pin="x") }} requirements: host: - - python >=3.6,<3.9 + - python >=3.6 - pip - setuptools-scm + - setuptools run: - - python >=3.6,<3.9 + - python >=3.6 - dadi + - demes + - demesdraw + - h5py ==3.10.0 - matplotlib-base - mpmath - nlopt - numpy - - pandas + - pandas <=2.2.2 - pillow - - ruamel.yaml - - scipy + - ruamel.yaml ==0.16.12 + - scipy <1.14 - networkx - moments - scikit-allel @@ -69,6 +73,7 @@ about: license_file: LICENSE summary: "Genetic Algorithm for Demographic Inference" doc_url: https://gadma.readthedocs.io/en/latest/ + dev_url: "https://github.com/ctlab/GADMA" extra: identifiers: diff --git a/recipes/gaftools/meta.yaml b/recipes/gaftools/meta.yaml new file mode 100644 index 0000000000000..ad29e06c99ed9 --- /dev/null +++ b/recipes/gaftools/meta.yaml @@ -0,0 +1,42 @@ +{% set name = "gaftools" %} +{% set version = "1.1.0" %} +{% set sha256 = "b04c1f7df479ab9a179b1709dec97dce054787f5fab8f2c2c38eb03df2e4a416" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + run_exports: + - {{ pin_compatible('gaftools', max_pin="x") }} + + +requirements: + host: + - python >=3.6 + - pip + - setuptools + run: + - python >=3.6 + - pysam + - pywfa ==0.5.1 + +test: + commands: + - gaftools -h + +about: + home: "https://github.com/marschall-lab/gaftools" + license: MIT + license_family: MIT + license_file: LICENSE + summary: 'gaftools is a fast and comprehensive toolkit designed for processing pangenome alignments in GAF format' + doc_url: "https://gaftools.readthedocs.io/en/latest/index.html" + dev_url: "https://github.com/marschall-lab" diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml index 8ed7d83d740ef..536b02f9c1d18 100644 --- a/recipes/gencove/meta.yaml +++ b/recipes/gencove/meta.yaml @@ -1,6 +1,6 @@ {% set name = "gencove" %} -{% set version = "2.24.0" %} -{% set sha256 = "1ec41ae1e663d7ab27b3c1e6af3eccb49e95120d084bae4c25305aab1126e7fb" %} +{% set version = "2.24.1" %} +{% set sha256 = "3c6d3c236dcad933fcb8298a394b84882398a577aa5f8c140ddefeabeb167513" %} package: name: {{ name }} diff --git a/recipes/gfastats/meta.yaml b/recipes/gfastats/meta.yaml index a08adf7d76b65..606f01e6dd06c 100644 --- a/recipes/gfastats/meta.yaml +++ b/recipes/gfastats/meta.yaml @@ -1,5 +1,5 @@ {% set name = "gfastats" %} -{% set version = "1.3.8" %} +{% set version = "1.3.9" %} package: name: {{ name }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/vgl-hub/gfastats/releases/download/v{{version}}/gfastats.v{{version}}-with_submodules.zip - sha256: e8e2eeef3156628606507d6d50a2be8f546bd1a4734d63ac87c61f84d6834481 + sha256: d98a14559ad3440ead7e6b04302ecaf1c44cffff40d64725d653b7e885a56a98 build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('gfastats', max_pin="x") }} @@ -43,4 +43,4 @@ extra: extended-base: true skip-lints: - uses_vcs_url - - missing_hash \ No newline at end of file + - missing_hash diff --git a/recipes/gnparser/meta.yaml b/recipes/gnparser/meta.yaml index 82ec7ca69faca..4f537929da200 100644 --- a/recipes/gnparser/meta.yaml +++ b/recipes/gnparser/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10.3" %} -{% set sha256 = "899661ab88b716b7c1e3c4430bfb388997e510b28961e0246c361407f34cf0d2" %} +{% set version = "1.11.0" %} +{% set sha256 = "9bf08647db16559f2b274086e468f54ce8108ef413fab5e4b745af90efccebea" %} package: name: "gnparser" @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('gnparser', max_pin="x") }} diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml index efce055df5c10..3be1717cb17c8 100644 --- a/recipes/goldrush/meta.yaml +++ b/recipes/goldrush/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: true # [py < 38 or win or py > 39] - number: 0 + number: 1 run_exports: {{ pin_subpackage("goldrush", max_pin="x") }} requirements: @@ -41,6 +41,7 @@ requirements: - gperftools - bc - snakemake + - numpy >=1.22.4 test: commands: diff --git a/recipes/gottcha2/meta.yaml b/recipes/gottcha2/meta.yaml index 50a0db70f10d7..29e33a06cc724 100644 --- a/recipes/gottcha2/meta.yaml +++ b/recipes/gottcha2/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GOTTCHA2" %} -{% set version = "2.1.8.6" %} +{% set version = "2.1.8.7" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: build: noarch: python number: 0 - script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation . + script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation --no-cache-dir . entry_points: - gottcha2 = cmd:gottcha2_command run_exports: @@ -16,12 +16,13 @@ build: source: url: https://github.com/poeli/GOTTCHA2/archive/refs/tags/{{ version }}.tar.gz - sha256: 18ae74fa448e837ade605676334c5c37cda07473a6cf0105937d8afe1b017359 + sha256: 52426b49dff96d5c17ac3f9e496df01846c519a41de0d0f2071a16a486ceefdf requirements: host: - python >=3.6 - pip + - setuptools run: - python >=3.6 - minimap2 >=2.17 diff --git a/recipes/gzrt/build.sh b/recipes/gzrt/build.sh new file mode 100644 index 0000000000000..c912bc43c9d6e --- /dev/null +++ b/recipes/gzrt/build.sh @@ -0,0 +1,58 @@ +#!/bin/bash + +# Exit on error +set -e + +if [ -z "$PREFIX" ]; then + echo "PREFIX environment variable not set" + exit 1 +fi + +export CFLAGS="${CFLAGS:-} -I${PREFIX}/include" +export LDFLAGS="${LDFLAGS:-} -L${PREFIX}/lib" +export CPATH="${PREFIX}/include" + +# If-body reserved to docker build +if [ ! -f "$(command -v cc)" ]; then + # Ensure that the CC environment variable is set (for compiler) + if [ -z "$CC" ]; then + echo "CC environment variable not set, but it is required." + exit 1 + fi + + # Create a temporary directory + mkdir -p "$SRC_DIR/bin" + + # Create a symlink named cc that points to $CC + CC_PATH="$(which "${CC}")" + if [ ! -x "${CC_PATH}" ]; then + echo "Could not find compiler at: ${CC_PATH}" + exit 1 + fi + ln -sf "${CC_PATH}" "${SRC_DIR}/bin/cc" + + # Prepend the temporary directory to the PATH + export PATH="${SRC_DIR}/bin:${PATH}" +fi + +if ! make; then + echo "Build failed" + exit 1 +fi + +if [ ! -f gzrecover ]; then + echo "Build did not produce gzrecover binary" + exit 1 +fi + +chmod 755 gzrecover + +if ! mkdir -p "$PREFIX/bin"; then + echo "Failed to create bin directory" + exit 1 +fi + +if ! cp gzrecover "$PREFIX/bin/"; then + echo "Failed to install gzrecover" + exit 1 +fi diff --git a/recipes/gzrt/gpl-2.0.txt b/recipes/gzrt/gpl-2.0.txt new file mode 100644 index 0000000000000..9efa6fbc96283 --- /dev/null +++ b/recipes/gzrt/gpl-2.0.txt @@ -0,0 +1,338 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Lesser General Public License instead.) You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. 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You may copy and distribute verbatim copies of the Program's +source code as you receive it, in any medium, provided that you +conspicuously and appropriately publish on each copy an appropriate +copyright notice and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + + 2. 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It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Moe Ghoul, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. diff --git a/recipes/gzrt/meta.yaml b/recipes/gzrt/meta.yaml new file mode 100644 index 0000000000000..703c3fd209dcb --- /dev/null +++ b/recipes/gzrt/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.8" %} # latest release on 2013-10-03 +{% set sha256 = "b0b7dc53dadd8309ad9f43d6d6be7ac502c68ef854f1f9a15bd7f543e4571fee" %} + +package: + name: gzrt + version: {{ version }} + +source: + url: https://www.urbanophile.com/arenn/hacking/gzrt/gzrt-{{ version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gzrt', max_pin="x.x") }} + +requirements: + build: + - {{ compiler("c") }} + - make + - zlib + host: + - zlib + +test: + commands: + - gzrecover -h + # Create and test with a corrupted gzip file + - echo "test" | gzip > test.gz + - dd if=/dev/zero of=test.gz bs=1 count=1 seek=5 conv=notrunc + - gzrecover test.gz || [[ $? -eq 1 ]] + +about: + home: https://www.urbanophile.com/arenn/hacking/gzrt + summary: "Unofficial build of the gzip Recovery Toolkit aka gzrecover" + license: GPL-2.0-only + license_family: GPL + license_file: gpl-2.0.txt + description: | + gzrecover is a program that will attempt to extract any readable data + out of a gzip file that has been corrupted. + dev_url: https://github.com/arenn/gzrt + +extra: + recipe-maintainers: + - mazzalab diff --git a/recipes/halfdeep/build.sh b/recipes/halfdeep/build.sh new file mode 100644 index 0000000000000..69df8bfa05cbd --- /dev/null +++ b/recipes/halfdeep/build.sh @@ -0,0 +1,28 @@ +#!/usr/bin/env bash + +set -o errexit +set -o nounset +set -o xtrace + +mkdir -vp "${PREFIX}/bin" + +# Define installation manifest +declare -A files=( + ["bam_depth.sh"]="0755" + ["halfdeep.sh"]="0755" + ["halfdeep.r"]="0755" + ["scaffold_lengths.py"]="0755" +) + +# Install files +for file in "${!files[@]}"; do + if [[ ! -f "$SRC_DIR/$file" ]]; then + echo "Source file $file not found in $SRC_DIR" >&2 + exit 1 + fi + + if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then + echo "Failed to install $file" >&2 + exit 1 + fi +done diff --git a/recipes/halfdeep/meta.yaml b/recipes/halfdeep/meta.yaml new file mode 100644 index 0000000000000..7cc7471ed8165 --- /dev/null +++ b/recipes/halfdeep/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "HalfDeep" %} +{% set version = "0.1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/richard-burhans/{{ name }}/archive/refs/tags/{{ version }}.zip + sha256: 308341c567298703fb99d4ceac7b34f0718cf6a37b02fc166f68d661a7f44f27 + +requirements: + run: + - bash + - coreutils + - gawk + - genodsp + - grep + - gzip + - minimap2 + - python >={{ python_min | default("3.9") }} + - r-base >={{ r_base | default("4.3.*") }} + - samtools + - sed + +build: + number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name|lower, max_pin="x.x") }} + +test: + commands: + - ${PREFIX}/bin/genodsp --help + +about: + home: https://github.com/richard-burhans/{{ name }} + summary: Automated detection of intervals covered at half depth by sequenced reads. + license: BSD-3-Clause + license_file: LICENSE + license_url: https://github.com/richard-burhans/{{ name }}/blob/master/LICENSE diff --git a/recipes/harpy/meta.yaml b/recipes/harpy/meta.yaml index 6e30e61e6e75f..a76e823eac517 100644 --- a/recipes/harpy/meta.yaml +++ b/recipes/harpy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.10" %} -{% set sha256 = "a2664cf94e89f1a1ab20519445c0649425ddf4c9204bdfe91cfc36a77e835f82" %} +{% set version = "1.11" %} +{% set sha256 = "e48308505e8ef9e6be2fdce8cb449f9fffe1aabcf1fb6b6e2aba94a8b00ccc71" %} package: name: harpy diff --git a/recipes/k8/build_failure.linux-aarch64.yaml b/recipes/k8/build_failure.linux-aarch64.yaml deleted file mode 100644 index 0f24706a1a3cb..0000000000000 --- a/recipes/k8/build_failure.linux-aarch64.yaml +++ /dev/null @@ -1,4 +0,0 @@ -recipe_sha: 751a182044682904040e221315daeec2db6609dd34a65b46fd328abc6bd46c37 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -category: CI unresponsive -reason: CPU at 100% for most of the build and timing out. Try in a separate PR. \ No newline at end of file diff --git a/recipes/k8/build_failure.osx-64.yaml b/recipes/k8/build_failure.osx-64.yaml deleted file mode 100644 index 29e18e3dfa6d2..0000000000000 --- a/recipes/k8/build_failure.osx-64.yaml +++ /dev/null @@ -1,106 +0,0 @@ -recipe_sha: 751a182044682904040e221315daeec2db6609dd34a65b46fd328abc6bd46c37 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tzfmt.o ../deps/icu-small/source/i18n/tzfmt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tzfmt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uregexc.o ../deps/icu-small/source/i18n/uregexc.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uregexc.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/measfmt.o ../deps/icu-small/source/i18n/measfmt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/measfmt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/brktrans.o ../deps/icu-small/source/i18n/brktrans.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/brktrans.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tmutamt.o ../deps/icu-small/source/i18n/tmutamt.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tmutamt.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/coptccal.o ../deps/icu-small/source/i18n/coptccal.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/coptccal.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/wintzimpl.o ../deps/icu-small/source/i18n/wintzimpl.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/wintzimpl.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/indiancal.o ../deps/icu-small/source/i18n/indiancal.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/indiancal.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_mapper.o ../deps/icu-small/source/i18n/number_mapper.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_mapper.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - 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x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_patternstring.o ../deps/icu-small/source/i18n/number_patternstring.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/number_patternstring.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/udat.o ../deps/icu-small/source/i18n/udat.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/udat.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tolowtrn.o ../deps/icu-small/source/i18n/tolowtrn.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/tolowtrn.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/numparse_impl.o ../deps/icu-small/source/i18n/numparse_impl.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/numparse_impl.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/unum.o ../deps/icu-small/source/i18n/unum.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/unum.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbtz.o ../deps/icu-small/source/i18n/rbtz.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/rbtz.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uni2name.o ../deps/icu-small/source/i18n/uni2name.cpp '-DV8_DEPRECATION_WARNINGS' '-DV8_IMMINENT_DEPRECATION_WARNINGS' '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DU_I18N_IMPLEMENTATION=1' '-DU_ATTRIBUTE_DEPRECATED=' '-DU_STATIC_IMPLEMENTATION=1' '-DUCONFIG_NO_SERVICE=1' '-DU_ENABLE_DYLOAD=0' '-DU_HAVE_STD_STRING=1' '-DUCONFIG_NO_BREAK_ITERATION=0' -I../deps/icu-small/source/i18n -I../deps/icu-small/source/common -O3 -gdwarf-2 -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/icui18n/deps/icu-small/source/i18n/uni2name.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/v8_bigint.stamp - touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/v8_heap_base.stamp - touch $SRC_DIR/node-v18.19.1/out/Release/obj.target/tools/v8_gypfiles/cppgc_base.stamp - touch 7c3e22e70fd7ad60278a99f71782417440fb78d1.intermediate - LD_LIBRARY_PATH=$SRC_DIR/node-v18.19.1/out/Release/lib.host:$SRC_DIR/node-v18.19.1/out/Release/lib.target:$LD_LIBRARY_PATH; export LD_LIBRARY_PATH; cd ../tools/v8_gypfiles; mkdir -p $SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/src/inspector/protocol $SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/include/inspector; /usr/local/bin/python3.11 ../../deps/v8/third_party/inspector_protocol/code_generator.py --jinja_dir ../../deps/v8/third_party --output_base "$SRC_DIR/node-v18.19.1/out/Release/obj/gen/inspector-generated-output-root/src/inspector" --config ../../deps/v8/src/inspector/inspector_protocol_config.json --config_value "protocol.path=../../deps/v8/include/js_protocol.pdl" --inspector_protocol_dir ../../deps/v8/third_party/inspector_protocol - In file included from ../deps/v8/src/libplatform/tracing/trace-writer.cc:14: - ../deps/v8/src/libplatform/tracing/recorder.h:17:10: fatal error: 'os/signpost.h' file not found - #include - ^~~~~~~~~~~~~~~ - 1 error generated. - make[1]: *** [tools/v8_gypfiles/v8_libplatform.target.mk:175: /opt/mambaforge/envs/bioconda/conda-bld/k8_1717953792721/work/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o] Error 1 - make[1]: *** Waiting for unfinished jobs.... - make: *** [Makefile:134: node] Error 2 - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-foreground-task-runner.o ../deps/v8/src/libplatform/default-foreground-task-runner.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-foreground-task-runner.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-job.o ../deps/v8/src/libplatform/default-job.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-job.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-platform.o ../deps/v8/src/libplatform/default-platform.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-platform.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/k8_1717953792721/work/conda_build.sh']' returned non-zero exit status 2. - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-worker-threads-task-runner.o ../deps/v8/src/libplatform/default-worker-threads-task-runner.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/default-worker-threads-task-runner.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/delayed-task-queue.o ../deps/v8/src/libplatform/delayed-task-queue.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/delayed-task-queue.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/task-queue.o ../deps/v8/src/libplatform/task-queue.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/task-queue.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-buffer.o ../deps/v8/src/libplatform/tracing/trace-buffer.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-buffer.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-config.o ../deps/v8/src/libplatform/tracing/trace-config.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-config.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-object.o ../deps/v8/src/libplatform/tracing/trace-object.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-object.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o ../deps/v8/src/libplatform/tracing/trace-writer.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/trace-writer.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/tracing-controller.o ../deps/v8/src/libplatform/tracing/tracing-controller.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/tracing/tracing-controller.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/worker-thread.o ../deps/v8/src/libplatform/worker-thread.cc '-D_GLIBCXX_USE_CXX11_ABI=1' '-DNODE_OPENSSL_CONF_NAME=nodejs_conf' '-DNODE_OPENSSL_HAS_QUIC' '-DICU_NO_USER_DATA_OVERRIDE' '-DV8_GYP_BUILD' '-DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64' '-D_DARWIN_USE_64_BIT_INODE=1' '-DOPENSSL_NO_PINSHARED' '-DOPENSSL_THREADS' '-DV8_TARGET_ARCH_X64' '-DV8_HAVE_TARGET_OS' '-DV8_TARGET_OS_MACOS' '-DV8_EMBEDDER_STRING="-node.28"' '-DENABLE_DISASSEMBLER' '-DV8_PROMISE_INTERNAL_FIELD_COUNT=1' '-DV8_SHORT_BUILTIN_CALLS' '-DOBJECT_PRINT' '-DV8_INTL_SUPPORT' '-DV8_ATOMIC_OBJECT_FIELD_WRITES' '-DV8_ENABLE_LAZY_SOURCE_POSITIONS' '-DV8_USE_SIPHASH' '-DV8_SHARED_RO_HEAP' '-DV8_WIN64_UNWINDING_INFO' '-DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH' '-DV8_ENABLE_SYSTEM_INSTRUMENTATION' '-DV8_ENABLE_WEBASSEMBLY' '-DV8_ENABLE_JAVASCRIPT_PROMISE_HOOKS' '-DV8_ALLOCATION_FOLDING' '-DV8_ALLOCATION_SITE_TRACKING' '-DV8_SCRIPTORMODULE_LEGACY_LIFETIME' '-DV8_ADVANCED_BIGINT_ALGORITHMS' -I../deps/v8 -I../deps/v8/include -O3 -gdwarf-2 -fstrict-aliasing -mmacosx-version-min=10.15 -arch x86_64 -Wall -Wendif-labels -W -Wno-unused-parameter -std=gnu17 -stdlib=libc -fno-rtti -fno-exceptions -fno-strict-aliasing -MMD -MF $SRC_DIR/node-v18.19.1/out/Release/.deps/$SRC_DIR/node-v18.19.1/out/Release/obj.target/v8_libplatform/deps/v8/src/libplatform/worker-thread.o.d.raw -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/k8-1.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c - rm 7c3e22e70fd7ad60278a99f71782417440fb78d1.intermediate -# Last 100 lines of the build log. -category: |- - compiler error diff --git a/recipes/konezumiaid/meta.yaml b/recipes/konezumiaid/meta.yaml index 5ead433a9586c..91121c8a30c31 100644 --- a/recipes/konezumiaid/meta.yaml +++ b/recipes/konezumiaid/meta.yaml @@ -1,5 +1,5 @@ {% set name = "KOnezumiAID" %} -{% set version = "0.3.1" %} +{% set version = "0.3.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/konezumiaid-{{ version }}.tar.gz - sha256: 78379cd1c923c5e6ae81fe0c0e84f6624b05ecca0cb87a73381431756e8a3489 + sha256: 7bc66fa4daa3fbe8d0c9f02fe1f594eeb8eb3fc722a788c2d31e290279218777 build: entry_points: diff --git a/recipes/lamps/meta.yaml b/recipes/lamps/meta.yaml new file mode 100644 index 0000000000000..928e649120589 --- /dev/null +++ b/recipes/lamps/meta.yaml @@ -0,0 +1,55 @@ +{% set name = "lamps" %} +{% set version = "1.0.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/lamps-{{ version }}.tar.gz + sha256: c85de92edcb4cd450aeebcb829729f163a02b3905146ef5208f911f38f2abe63 + +build: + entry_points: + - lamp = lamp.__main__:main + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage('lamps', max_pin="x") }} + +requirements: + host: + - python >=3.8 + - setuptools >=61.0 + - wheel + - pip + run: + - python >=3.8 + - numpy + - scipy + - pandas + - pyside6 + - pyteomics + - openpyxl + - pyjanitor + +test: + imports: + - lamp + commands: + - pip check + - lamp --help + requires: + - pip + +about: + home: https://pypi.org/project/lamps/ + summary: Liverpool Annotation of metabolites using Mass Spectrometry + dev_url: https://github.com/wanchanglin/lamp + license: GPL-3.0-or-later + license_file: LICENSE + +extra: + recipe-maintainers: + - harryln-1 diff --git a/recipes/locityper/build.sh b/recipes/locityper/build.sh index 0698575530e7c..d1c7c01febf6a 100644 --- a/recipes/locityper/build.sh +++ b/recipes/locityper/build.sh @@ -8,6 +8,10 @@ fi export C_INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" +if [[ `uname` == 'Darwin' ]]; then + export MACOSX_DEPLOYMENT_TARGET=10.11 +fi + git clone https://github.com/smarco/WFA2-lib WFA2 # build statically linked binary with Rust diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index c9c450090f4ed..393549ad8f4ce 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "locityper" %} -{% set version = "0.16.12" %} +{% set version = "0.17.3" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: 0bd3a82c1df6de921ed477edfca4ffb5017cf194807e358e482b49afba867dd7 + sha256: d9ecc464a4394a0523afd6ba4c5f7bf80fe44ca15926cca1075ac70cd14b9255 build: number: 0 diff --git a/recipes/longcallr_nn/meta.yaml b/recipes/longcallr_nn/meta.yaml index 387e4451d9830..a76c1551439cf 100644 --- a/recipes/longcallr_nn/meta.yaml +++ b/recipes/longcallr_nn/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 noarch: python entry_points: - longcallR_nn=longcallR_nn.longcallR_nn:main @@ -23,16 +23,17 @@ build: requirements: host: - pip - - python 3.9.* + - python >=3.9,<3.11 run: - - python 3.9.* - - numpy 1.21.0 - - pyyaml - - pysam - - tensorboardX - - pytorch 1.13.* - - torchvision - - torchmetrics + - python >=3.9,<3.11 + - requests + - numpy >=1.21.0 + - pyyaml >=5.3 + - pysam >=0.16 + - tensorboardX >=2.2 + - pytorch >=1.13 + - torchvision >=0.14 + - torchmetrics >=0.9 test: commands: diff --git a/recipes/matchms/meta.yaml b/recipes/matchms/meta.yaml index 6485c985ee7c8..5d730e31b4a31 100644 --- a/recipes/matchms/meta.yaml +++ b/recipes/matchms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "matchms" %} -{% set version = "0.27.0" %} +{% set version = "0.28.2" %} package: name: "{{ name|lower }}" @@ -7,10 +7,10 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 96d15fbc006c90ac306e91b9fc609255108c48536094d2a55502f6a2e65fbce8 + sha256: 63b0c3af5cbdc6367a50ecae002e832f96c96d5a7073774b608984ce2b515d46 build: - number: 1 + number: 0 script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" noarch: python run_exports: @@ -19,26 +19,26 @@ build: requirements: host: - pip - - python >=3.9,<3.13 + - python >=3.10,<3.13 - poetry-core run: - deprecated >=1.2.14 - lxml >=4.9.3,<5 - matplotlib-base >=3.7 - - networkx >=3.0 - - numba >=0.57.1,<0.60 - - numpy >1.22,<1.27 + - networkx >=3.4.2 + - numba >=0.60.0 + - numpy >=2.0.0 - pickydict >=0.4.0 - pyteomics >=4.6 - - python >=3.9,<3.13 + - python >=3.10,<3.13 - pyyaml >=6.0.1 - - rdkit >=2023.9.6 + - rdkit >=2024.3.5 - requests >=2.31.0 - - scipy >=1.11 - - sparsestack >=0.4.1 + - scipy >=1.14.1 + - sparsestack >=0.6.0 - tqdm >=4.65.0 - pillow !=9.4.0 - - pandas >=2.0.3 + - pandas >=2.2.3 - pubchempy test: diff --git a/recipes/melon/meta.yaml b/recipes/melon/meta.yaml index bb85221963f0a..f8d22b73e9bfe 100644 --- a/recipes/melon/meta.yaml +++ b/recipes/melon/meta.yaml @@ -1,5 +1,5 @@ {% set name = "melon" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://github.com/xinehc/melon/archive/refs/tags/v{{ version }}.tar.gz - sha256: 3020c20f8619aeeb254a52eb8822dab3689956b3e218450cd8506a42f263f7f4 + sha256: 3b3d09801212282b5ebb8030976d49361484031460c53f6440c61706af90cd63 build: noarch: python @@ -19,6 +19,7 @@ build: requirements: host: - pip + - setuptools - python >=3.7 run: - python >=3.7 @@ -40,7 +41,7 @@ about: home: https://github.com/xinehc/melon license: MIT license_family: MIT - summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification' + summary: 'Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes' extra: recipe-maintainers: diff --git a/recipes/metaphor/meta.yaml b/recipes/metaphor/meta.yaml index 71a95ce8a10f9..a73669ed4ed8d 100644 --- a/recipes/metaphor/meta.yaml +++ b/recipes/metaphor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "metaphor" %} -{% set version = "1.7.13" %} +{% set version = "1.7.14" %} package: name: "{{ name|lower }}" @@ -7,20 +7,22 @@ package: source: url: https://github.com/vinisalazar/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 88f959b4eb30cb7794d361015b386220cc5a0e1c0e09d710a575890febed57d9 + sha256: 86025b04ffa49d0f6430c02bba06533ce30e4ea5e45daeac3564d4be3a98bb84 build: number: 0 noarch: python + entry_points: + - metaphor = metaphor.cli.cli:main run_exports: - {{ pin_subpackage(name, max_pin="x") }} script: - - "{{ PYTHON }} -m pip install . -vv" + - "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" requirements: host: - pip - - python >=3.9 + - python >=3.9,<3.12 run: - jinja2 - networkx @@ -28,7 +30,7 @@ requirements: - python >=3.9,<3.12 - pyyaml - requests - - snakemake >=7.5 + - snakemake-minimal >=7.5,<8.0 - snakemake-wrapper-utils - tqdm - zstandard diff --git a/recipes/minimac4/build.sh b/recipes/minimac4/build.sh new file mode 100644 index 0000000000000..d3b62199c6ca3 --- /dev/null +++ b/recipes/minimac4/build.sh @@ -0,0 +1,49 @@ +#!/bin/bash +set -euo pipefail + +echo "Building Minimac4 version ${PKG_VERSION}" + +# Set CXXFLAGS to include the correct path to lzma.h and LDFLAGS to include the path to liblzma +export CXXFLAGS="-I${PREFIX}/include -I${PREFIX}/lib" +export LDFLAGS="-L${PREFIX}/lib -llzma" +CMAKE_MAKE_PROGRAM="$(which make)" +CMAKE_C_COMPILER="${CC}" +CMAKE_CXX_COMPILER="${CXX}" + +export CMAKE_MAKE_PROGRAM +export CMAKE_C_COMPILER +export CMAKE_CXX_COMPILER + +# Set up dependencies and directories +if [ ! -f ./requirements.txt ]; then + echo "Error: requirements.txt not found" + exit 1 +fi +cget ignore xz || exit 1 +cget install -f ./requirements.txt || exit 1 + +cmake --version +mkdir -p build || exit 1 +cd build || exit 1 + +cmake \ + -DBUILD_TESTS=1 \ + -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake \ + -DCMAKE_CXX_FLAGS="${CXXFLAGS}" \ + -DCMAKE_EXE_LINKER_FLAGS="${LDFLAGS}" \ + -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} \ + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} \ + -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX=${PREFIX} \ + -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \ + -DCPACK_GENERATOR="STGZ" \ + -DCPACK_PACKAGE_CONTACT="csg-devel@umich.edu" \ + .. + +make || exit 1 +make install || exit 1 +make CTEST_OUTPUT_ON_FAILURE=1 test || exit 1 +echo "Minimac4 installation completed successfully" + +cd .. || exit 1 diff --git a/recipes/minimac4/meta.yaml b/recipes/minimac4/meta.yaml new file mode 100644 index 0000000000000..889e9cbc3f5d8 --- /dev/null +++ b/recipes/minimac4/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "4.1.6" %} + +package: + name: minimac4 + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage('minimac4', max_pin='x.x.x') }} + +source: + url: https://github.com/statgen/Minimac4/archive/refs/tags/v{{ version }}.tar.gz + sha256: 0bce8d6edbf5d5d944b19c4e36403d0bc1d18f2d6003d88e01086488c3eb9333 + +requirements: + build: + - make + - cmake >=3.24 + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - cget + host: + - bcftools >=1.20 + - zlib + - savvy ==2.1.0 + - xz + run: + - cget + +test: + commands: + - minimac4 --help + - minimac4 --version + +about: + home: https://github.com/statgen/Minimac4 + license: GPL-3.0-or-later + license_file: LICENSE + summary: "Computationally efficient genotype imputation" + description: "Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3." diff --git a/recipes/minute/meta.yaml b/recipes/minute/meta.yaml index 8ce2b630e521a..aa0fbee72cd69 100644 --- a/recipes/minute/meta.yaml +++ b/recipes/minute/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.9.0" %} +{% set version = "0.10.0" %} package: name: minute @@ -6,21 +6,22 @@ package: source: url: https://github.com/elsasserlab/minute/archive/refs/tags/v{{ version }}.tar.gz - sha256: bac0252f635ff015d80abd35375407ccf48b12babd947f900889d6475f2cac13 + sha256: f784a571601ac2e673fe0783b13e9b7ef8ba8d1e4bab7f48aff67365e607f0fd build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('minute', max_pin='x.x') }} requirements: host: - pip - - python >=3.8 + - python >=3.7 + - setuptools run: - - python >=3.8 + - python >=3.7 - ruamel.yaml - snakemake-minimal >=7.22.0 - samtools >=1.13 @@ -50,8 +51,11 @@ test: about: home: https://github.com/elsasserlab/minute/ license: MIT + license_family: MIT + license_file: LICENSE summary: MINUTE-ChIP data analysis workflow - + dev_url: https://github.com/elsasserlab/minute + doc_url: https://minute.readthedocs.io/en/latest extra: recipe-maintainers: - marcelm diff --git a/recipes/ms2deepscore/meta.yaml b/recipes/ms2deepscore/meta.yaml index 055b6280d4790..2dd1a9aedceb0 100644 --- a/recipes/ms2deepscore/meta.yaml +++ b/recipes/ms2deepscore/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ms2deepscore" %} -{% set version = "2.3.0" %} -{% set sha256 = "fd62d373aa53944583bd7b0df324015198ea598a2def9cba9f13afd0acd09b18" %} +{% set version = "2.4.0" %} +{% set sha256 = "50c5827b0e6a40a29be270bcd9dd3873f0ef1094d8d9c06b354f09f67110fd56" %} package: name: {{ name|lower }} diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml index f52e85ac70a5e..1bd528fba686b 100644 --- a/recipes/muscle/meta.yaml +++ b/recipes/muscle/meta.yaml @@ -1,5 +1,5 @@ {% set name = "muscle" %} -{% set version = "5.2" %} +{% set version = "5.3" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7aff1473241a36da94a88f37920a343fae91d2b6faae22e15c06591d1d0339b6 + sha256: 74b22a94e630b16015c2bd9ae83aa2be2c2048d3e41f560b2d4a954725c81968 patches: - support-linux-aarch64.patch @@ -21,11 +21,16 @@ requirements: build: - {{ compiler('cxx') }} - llvm-openmp # [osx] + - macports-legacy-support # [osx] - make test: + files: + - test_data.fna commands: - - muscle -version + - muscle --version + - muscle --help + about: home: https://github.com/rcedgar/muscle license: GPL-3.0-only diff --git a/recipes/muscle/run_test.sh b/recipes/muscle/run_test.sh new file mode 100644 index 0000000000000..3fad89ae2e7cd --- /dev/null +++ b/recipes/muscle/run_test.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +muscle -msastats test_data.fna +muscle -super5 test_data.fna -output test_output.fna +cat test_output.fna diff --git a/recipes/muscle/test_data.fna b/recipes/muscle/test_data.fna new file mode 100644 index 0000000000000..864b3f67398da --- /dev/null +++ b/recipes/muscle/test_data.fna @@ -0,0 +1,6 @@ +>1 +GKGDP +>2 +MQDRVK +>3 +IKKPL diff --git a/recipes/notramp/meta.yaml b/recipes/notramp/meta.yaml index ac4aeed99c8ad..256a951ed7a91 100644 --- a/recipes/notramp/meta.yaml +++ b/recipes/notramp/meta.yaml @@ -1,5 +1,5 @@ {% set name = "notramp" %} -{% set version = "1.0.5" %} +{% set version = "1.1.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: de54fae8cc4c66dcd8abc94ae88957aa533cb8e2e6764e847afa26fbe4b36ec9 + sha256: d17dafed1f9afa119c48aca5486c59049774590ca5b90b6802a011d9eaec85ca build: number: 0 @@ -15,6 +15,8 @@ build: - notramp = notramp.notramp_main:run_notramp script: "{{ PYTHON }} -m pip install . -vv" noarch: python + run_exports: + - {{ pin_subpackage("notramp", max_pin="x") }} requirements: host: diff --git a/recipes/ntstat/meta.yaml b/recipes/ntstat/meta.yaml index b68ab46df1dd5..1a00b3d7d9d77 100644 --- a/recipes/ntstat/meta.yaml +++ b/recipes/ntstat/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0" %} +{% set version = "1.0.1" %} package: name: ntstat @@ -6,7 +6,7 @@ package: source: url: https://github.com/bcgsc/ntStat/releases/download/v{{ version }}/ntStat-{{ version }}.tar.gz - sha256: cbdf691033727466aaa774c5b9a7fc549448280b53f59579d1a43d9e943f9abd + sha256: 4cf215c15c2b1035c40a453372e39c3a87c37c4b09b5716ef5a07bba96f9cb99 build: number: 0 diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 1650e634f7841..c7fe2167f1b4e 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.11.25" %} -{% set sha256 = "f808922c851b81568107d8013344f233dddbbd9d0c69313a46c3c9f97ef42edd" %} +{% set version = "2.12.2" %} +{% set sha256 = "1f5f961a2c8d04857bc3a63ae165254501e806ff84dfff39780ea0415505a4c4" %} package: name: {{ name|lower }} diff --git a/recipes/orthodb/build.sh b/recipes/orthodb/build.sh new file mode 100644 index 0000000000000..5b807e129ac0a --- /dev/null +++ b/recipes/orthodb/build.sh @@ -0,0 +1,2 @@ +#!/bin/bash +$PYTHON -m pip install . --no-deps --ignore-installed -vv diff --git a/recipes/orthodb/meta.yaml b/recipes/orthodb/meta.yaml new file mode 100644 index 0000000000000..144090650d1e4 --- /dev/null +++ b/recipes/orthodb/meta.yaml @@ -0,0 +1,56 @@ +{% set name = "orthodb" %} +{% set version = "0.9.1" %} +{% set sha256 = "366160d5924870b37b0e86456eaac667ae194745fe78e16ede25f29299e34870" %} + +package: + name: {{ name }} + version: {{ version }} + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('orthodb', max_pin="x") }} + +source: + url: https://gitlab.com/ezlab/orthodb_py/-/archive/{{ version }}/orthodb_py-{{ version }}.tar.gz + sha256: {{ sha256 }} + +files: + - LICENSE + +requirements: + build: + - python >=3.7 + - pip + - setuptools + host: + - python >=3.7 + - pip + - setuptools + run: + - python >=3.7 + - requests + +test: + commands: + - python -c 'import orthodb' + - python -c 'from orthodb import OdbAPI' + +about: + home: https://www.ezlab.org/orthodb_v12_userguide.html + license: GPL3 + license_family: GPL3 + license_file: LICENSE + summary: Interface to OrthoDB REST API. + description: Python interface to OrthoDB REST API with some additional functionality. + dev_url: https://gitlab.com/ezlab/orthodb_py + doc_url: https://www.ezlab.org/orthodb_v12_userguide.html#api + +extra: + identifiers: + - biotools:orthodb + - doi:10.1093/nar/gkac996 + - PMID:36350662 + recipe-maintainers: + - ftegenfe diff --git a/recipes/pangolin/meta.yaml b/recipes/pangolin/meta.yaml index 8a8e2c1ced076..49e39138cca80 100644 --- a/recipes/pangolin/meta.yaml +++ b/recipes/pangolin/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.3" %} +{% set version = "4.3.1" %} package: name: pangolin @@ -6,27 +6,29 @@ package: source: url: https://github.com/cov-lineages/pangolin/archive/refs/tags/v{{ version }}.tar.gz - sha256: daf13c111799943b05bc2c8eee8deb2316e1347ca8f40f0b40d22cdbcc72e3c1 + sha256: 79f958cfc1b3a01144b138b9ca34ab010aa4ec72499a29ea41acaa57b0bfe7c0 build: - number: 2 + number: 0 noarch: python - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . + run_exports: + - {{ pin_subpackage('pangolin', max_pin="x") }} requirements: host: - python >=3.7 - pip + - setuptools run: - python >=3.7 - - biopython ==1.74 + - biopython >=1.74 - pandas >=1.0.1 - - tabulate - joblib >=0.11 - - scikit-learn <1.3.0 + - scikit-learn >=0.23.1,<1.3.0 - pulp >=2 - minimap2 >=2.16 - - snakemake-minimal >=5.13,<=7.30.1 + - snakemake-minimal >=5.13,!=7.30.1,<8 - gofasta - usher >=0.6.2 - ucsc-fatovcf >=426 diff --git a/recipes/pangolin/run_test.py b/recipes/pangolin/run_test.py index 61701e399aa4b..56c68067a019c 100644 --- a/recipes/pangolin/run_test.py +++ b/recipes/pangolin/run_test.py @@ -2,10 +2,12 @@ from pathlib import Path from subprocess import run, PIPE, STDOUT +import sys import pangolin test_data = Path(pangolin.__file__).parent / 'data/reference.fasta' cmd = ['pangolin', str(test_data)] pangolin_proc = run(cmd, stdout=PIPE, stderr=STDOUT) -assert b'Output file written to' in pangolin_proc.stdout, pangolin_proc.stdout +print(pangolin_proc.stdout.decode(), file=sys.stderr) +assert b'Output file written to' in pangolin_proc.stdout diff --git a/recipes/perl-ole-storage_lite/meta.yaml b/recipes/perl-ole-storage_lite/meta.yaml index 32d74e19280f0..0656e9a786df7 100644 --- a/recipes/perl-ole-storage_lite/meta.yaml +++ b/recipes/perl-ole-storage_lite/meta.yaml @@ -1,19 +1,19 @@ {% set name = "perl-ole-storage_lite" %} -{% set version = "0.20" %} -{% set sha256 = "ab18a6171c0e08ea934eea14a0ab4f3a8909975dda9da42124922eb41e84f8ba" %} +{% set version = "0.22" %} +{% set sha256 = "d0566d6c29d397ea736379dc515c36849f6b97107cf700ba8250505c984cf965" %} package: name: {{ name }} version: {{ version }} source: - url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.20.tar.gz + url: https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.22.tar.gz sha256: {{ sha256 }} # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: - number: 1 + number: 0 noarch: generic run_exports: weak: diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 33d901868c12f..940dad736add2 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -1,27 +1,27 @@ {% set name = "PhaBOX" %} -{% set version = "2.1.0" %} +{% set version = "2.1.5" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 0ffe4da03ccc2aac77c17866033ce513f72a5ecdf9df108abbcdbfced438b04c + url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: 875124cd1568fcb706662e7f86ff7e1ef79b38944156c8c5d0b1b329d983d73a build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - - phabox2 = phabox2.phabox2:main + - phabox2=phabox2.phabox2:main run_exports: - {{ pin_subpackage('phabox', max_pin="x.x") }} requirements: host: - - pip - python >=3.8 + - pip - setuptools run: - python >=3.8 @@ -39,23 +39,28 @@ requirements: - scipy >=1.14 - seaborn-base >=0.13.2 - transformers >=4 - + - blast >=2.16.0 + - diamond <=0.9.14 + - mcl >=22.282 + - accelerate >=1.0.1 + test: commands: - phabox2 --help about: - home: "https://phage.ee.cityu.edu.hk" + home: https://github.com/KennthShang/PhaBOX license: "AFL-3.0" license_family: OTHER - license_file: "LICENSE.md" - summary: "Phage BOX is a Python library for phage-related tasks." + license_file: "LICENSE.md" + summary: Virus identification and analysis tool set dev_url: "https://github.com/KennthShang/PhaBOX" doc_url: "https://github.com/KennthShang/PhaBOX/wiki" extra: recipe-maintainers: - - bernt-matthias + - SHANG Jiayu + - PENG Cheng identifiers: - doi:10.1093/bioadv/vbad101 - biotools:phabox diff --git a/recipes/polap/build.sh b/recipes/polap/build.sh index 343b7d9d0f89f..fd7226afabb7c 100644 --- a/recipes/polap/build.sh +++ b/recipes/polap/build.sh @@ -6,14 +6,72 @@ files=(polap polap-conda-environment-fmlrc.yaml polap-conda-environment.yaml polap-mt.1.c70.3.faa - polap-parsing.sh polap-pt.2.c70.3.faa - polap.sh - run-polap-genes.R - run-polap-jellyfish.R - run-polap-mtcontig.R run-polap-ncbitools - run-polap-pairs.R) + polap-command-completion.sh + polap-constants.sh + polap-function-set-variables.sh + polap-git-hash-version.sh + polap-parsing.sh + polap-test-variables.sh + polap-variables-common.sh + polap-variables-main.sh + polap-variables-mtcontigs.sh + polap-version.sh + run-polap-function-annotate-contig.sh + run-polap-function-annotate.sh + run-polap-function-archive.sh + run-polap-function-assemble.sh + run-polap-function-bioproject.sh + run-polap-function-include.sh + run-polap-function-log.sh + run-polap-function-menus.sh + run-polap-function-miscellaneous.sh + run-polap-function-mtdna.sh + run-polap-function-oga.sh + run-polap-function-polishing.sh + run-polap-function-seeds.sh + run-polap-function-template.sh + run-polap-function-utilities.sh + run-polap-function-wga.sh + run-polap-sh-create-depth-file.sh + run-polap-sh-half-cut.sh + run-polap-sh-minimap2-paf2tab.sh + run-polap-py-find-cc.py + run-polap-py-select-mtdna-2-nx-find-circular-path.py + run-polap-py-select-mtdna-2-nx-simple-cycles.py + run-polap-pairs.R + run-polap-r-assemble-bioproject-3-length-match.R + run-polap-r-blast-mtdna-1-determine-gene.R + run-polap-r-bridge.R + run-polap-r-cc2mtcontig.R + run-polap-r-depth-distribution.R + run-polap-r-depthfilter-gfa.R + run-polap-r-determine-depth-range.R + run-polap-r-determine-depth-range_1.R + run-polap-r-determine-depth-range_2.R + run-polap-r-determine-depth-range_3.R + run-polap-r-determine-depth-range_4.R + run-polap-r-determine-depth-range_5.R + run-polap-r-edges-stats.R + run-polap-r-final-filter-mtcontig.R + run-polap-r-final-mtcontig.R + run-polap-r-final-seed-mtcontig.R + run-polap-r-genes-bed4.R + run-polap-r-genes.R + run-polap-r-get-bioproject-1.R + run-polap-r-jellyfish.R + run-polap-r-mtcontig-contig.R + run-polap-r-mtcontig.R + run-polap-r-pairs.R + run-polap-r-plastid-determine-depth-range.R + run-polap-r-plot-mtdna.R + run-polap-r-prepare-cc.R + run-polap-r-preselect-annotation.R + run-polap-r-select-mtdna-1-nx-gfa-links.R + run-polap-r-template.R + run-polap-r-test-reads-bar-graph.R + polap.sh) for i in "${files[@]}"; do cp src/$i $PREFIX/bin @@ -21,4 +79,3 @@ done chmod +x $PREFIX/bin/polap chmod +x $PREFIX/bin/polap.sh -chmod +x $PREFIX/bin/run-polap-* diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml index eacc9680c84a3..17890cfb02e16 100644 --- a/recipes/polap/meta.yaml +++ b/recipes/polap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "polap" %} -{% set version = "0.2.6" %} -{% set sha256 = "6d9b5ffc26ce6feeaa6119d0dda57e07af9e9def55e5510b0ddf237699b15948" %} +{% set version = "0.3.7.1" %} +{% set sha256 = "c2a119c986035519b8252f4d85c91cfa060371ee0decc8c5d400b87428a81cfe" %} package: name: "{{ name }}" @@ -20,33 +20,37 @@ requirements: run: - python - flye >=2.9.2 - - seqkit - minimap2 >=2.24 - - blast + - seqkit - bedtools - seqtk - - bioawk - - entrez-direct - - sra-tools - csvtk - - gfastats - kmer-jellyfish - - clustalw + - blast + - entrez-direct + - sra-tools - samtools - - assembly-stats - orthofinder - bioconductor-ggtree - - perl-xml-libxml - - icu - - libxml2 - - perl - - r-base + - networkx + - pandas + - gfatools + - r-optparse - r-dplyr - r-readr - - r-optparse - r-stringr - r-tidyr - parallel + - r-base + - bioawk + - assembly-stats + - progressivemauve + - clustalw + - gfastats + - perl-xml-libxml + - icu + - libxml2 + - perl test: commands: diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 802e0ca68a124..b75e51baa76af 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.7.0" %} +{% set version = "2.7.1" %} {% set name = "PopPUNK" %} package: @@ -7,12 +7,12 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067 + sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788 build: number: 0 - skip: true # [py < 38] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + skip: True # [py < 38] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - poppunk = PopPUNK.__main__:main - poppunk_assign = PopPUNK.assign:main @@ -27,13 +27,12 @@ build: requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - {{ compiler('fortran') }} - - llvm-openmp # [osx] - - libgomp # [linux64] - cmake >=3.18 - make + - llvm-openmp # [osx] + - libgomp # [linux] host: # python - python @@ -64,7 +63,6 @@ requirements: - treeswift - requests # C++ extension - - zlib # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool. - xorg-libxi - xorg-libxcursor @@ -80,7 +78,6 @@ test: imports: - PopPUNK - poppunk_refine - commands: - poppunk --help - poppunk_assign --help @@ -92,16 +89,17 @@ test: - poppunk_lineages_from_strains --help about: - home: https://poppunk.bacpop.org/ - license: Apache-2.0 + home: "https://poppunk.bacpop.org" + license: "Apache-2.0" license_family: APACHE + license_file: LICENSE summary: 'PopPUNK (POPulation Partitioning Using Nucleotide Kmers)' + dev_url: "https://github.com/bacpop/PopPUNK" + doc_url: "https://poppunk.bacpop.org/index.html" extra: identifiers: - doi:10.1101/gr.241455.118 - # enabling this would require arm64 packages for: mandrake, pp-sketchlib, - # rapidnj - # additional-platforms: - # - linux-aarch64 - # - osx-arm64 + - biotools:poppunk + additional-platforms: + - osx-arm64 diff --git a/recipes/proteinortho/build.sh b/recipes/proteinortho/build.sh index 65cbd9e704393..ea9644d67ef30 100755 --- a/recipes/proteinortho/build.sh +++ b/recipes/proteinortho/build.sh @@ -1,12 +1,17 @@ #!/bin/bash +mkdir -p $PREFIX/bin + +export INCLUDES="-I${PREFIX}/include" +export LIBPATH="-L${PREFIX}/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CXXFLAGS="${CXXFLAGS} -O3 -I$PREFIX/include" export STATIC="FALSE" -if [ `uname` == Darwin ]; then + +if [[ `uname` == Darwin ]]; then export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" -# export STATIC="TRUE" fi make clean -make CC=$CC CXX=$CXX STATIC=$STATIC all -j${CPU_COUNT} -mkdir -p $PREFIX/bin -make install PREFIX=$PREFIX/bin/ +make CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" STATIC="${STATIC}" all -j"${CPU_COUNT}" +make install PREFIX="${PREFIX}/bin/" diff --git a/recipes/proteinortho/meta.yaml b/recipes/proteinortho/meta.yaml index 0d1fa24143b21..be6e3274c7f74 100755 --- a/recipes/proteinortho/meta.yaml +++ b/recipes/proteinortho/meta.yaml @@ -1,6 +1,6 @@ {% set name = "proteinortho" %} -{% set version = "6.3.2" %} -{% set sha256 = "3b3c58e814ca10f77a25954b0bcddc479b9f61682f3dc5c93d85b07f109342a4" %} +{% set version = "6.3.3" %} +{% set sha256 = "989eed292e6e65c3725d4395cb7aed3c59754b5dc60d4a1e034aa1c4a6504c6c" %} package: name: {{ name }} @@ -13,21 +13,22 @@ source: build: number: 0 run_exports: - - {{ pin_subpackage('proteinortho', max_pin="x.x.x") }} - + - {{ pin_subpackage('proteinortho', max_pin="x") }} requirements: build: - make - {{ compiler('cxx') }} - - {{ compiler('fortran') }} - - llvm-openmp # [osx] - - libgomp # [linux] + - {{ compiler('fortran') }} - cmake host: + - llvm-openmp # [osx] + - libgomp # [linux] - liblapack - blis run: + - llvm-openmp # [osx] + - libgomp # [linux] - perl - python - diamond >=0.9.29 @@ -42,13 +43,20 @@ test: - proteinortho_grab_proteins.pl -help about: - home: https://gitlab.com/paulklemm_PHD/proteinortho/ + home: "https://gitlab.com/paulklemm_PHD/proteinortho" license: GPL-3.0-only license_family: GPL license_file: LICENSE summary: "Proteinortho is a tool to detect orthologous genes within different species." + dev_url: "https://gitlab.com/paulklemm_PHD/proteinortho" + doc_url: "https://gitlab.com/paulklemm_PHD/proteinortho/-/blob/master/README.md" extra: identifiers: - biotools:proteinortho - doi:10.3389/fbinf.2023.1322477 + - usegalaxy-eu:proteinortho + - usegalaxy-eu:proteinortho_summary + - usegalaxy-eu:proteinortho_grab_proteins + additional-platforms: + - linux-aarch64 diff --git a/recipes/pycomo/meta.yaml b/recipes/pycomo/meta.yaml index af10fd414d0aa..a2d092fe9f69e 100644 --- a/recipes/pycomo/meta.yaml +++ b/recipes/pycomo/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pycomo" %} -{% set version = "0.2.2" %} +{% set version = "0.2.4" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pycomo-{{ version }}.tar.gz - sha256: 242973127addd422bcfabc8db79caaaa88c3a1e87f86b735a4de5449abe99331 + sha256: 5da3c1e85f0f0ca7b0fda240a7badb9ed8a84d65ec338c4334a0895463b1fb49 build: entry_points: diff --git a/recipes/pyfamsa/meta.yaml b/recipes/pyfamsa/meta.yaml index 5cb5faa479d92..a08d3a6682906 100644 --- a/recipes/pyfamsa/meta.yaml +++ b/recipes/pyfamsa/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyfamsa" %} -{% set version = "0.5.2" %} +{% set version = "0.5.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 5715eccfaf0ac38f9eba951285de900086e10007b0e2508e3735879d7e4e5fce + sha256: d5492e885c71dedfd3ddb1fc16b02981388f7fcb7dbb152c37b8bffa5f760ce5 build: number: 0 @@ -19,11 +19,13 @@ requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} + - cmake + - make host: - python - pip - cython - - semantic_version + - scikit-build-core - scoring-matrices >=0.2 run: - python diff --git a/recipes/pyjess/meta.yaml b/recipes/pyjess/meta.yaml new file mode 100644 index 0000000000000..82ed92722ed9e --- /dev/null +++ b/recipes/pyjess/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "pyjess" %} +{% set version = "0.3.3" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: dc7d9a39ce75112d672780a57a9629afb3a78af6194028d8fad7a7138024de6f + +build: + number: 0 + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv" + run_exports: + - {{ pin_subpackage("pyjess", max_pin="x.x") }} + +requirements: + build: + - {{ compiler('c') }} + - cmake >=3.20 + - make + host: + - python + - pip + - cython + - scikit-build-core + run: + - python + +test: + imports: + - {{ name }} + commands: + - python -m unittest -vv {{ name }}.tests + +about: + home: "https://github.com/althonos/pyjess" + license: "MIT" + license_family: MIT + license_file: COPYING + summary: "Cython bindings and Python interface to JESS, a 3D template matching software." + doc_url: "https://pyjess.readthedocs.org" + dev_url: "https://github.com/althonos/pyjess" + +extra: + recipe-maintainers: + - althonos + additional-platforms: + - linux-aarch64 + - osx-arm64 diff --git a/recipes/pyopenms/conda_build_config.yaml b/recipes/pyopenms/conda_build_config.yaml deleted file mode 100644 index dd7f1933d9e4e..0000000000000 --- a/recipes/pyopenms/conda_build_config.yaml +++ /dev/null @@ -1,19 +0,0 @@ -python: - - 3.9.* - - 3.10.* - - 3.11.* - - 3.12.* -python_impl: - - cpython - - cpython - - cpython - - cpython -numpy: - - 1.23.* - - 1.23.* - - 1.23.* - - 1.26.* -zip_keys: - - python - - python_impl - - numpy diff --git a/recipes/pyopenms/meta.yaml b/recipes/pyopenms/meta.yaml index f156ccddb0a36..59cf39da0d5d7 100644 --- a/recipes/pyopenms/meta.yaml +++ b/recipes/pyopenms/meta.yaml @@ -17,7 +17,7 @@ source: build: skip: True # [py2k or osx] - number: 0 + number: 1 run_exports: - {{ pin_subpackage("pyopenms", max_pin="x.x") }} @@ -35,13 +35,13 @@ requirements: - xerces-c - boost-cpp - qt-main >=5.15.8 - - python {{ python }} + - python >=3.9,<3.13 - cython >=0.25.2 - autowrap >=0.22.10 - setuptools - wheel - pip - - numpy {{ numpy }} + - numpy >=1.23.* - pandas - matplotlib-base - sysroot_linux-64 =2.17 # [linux] @@ -54,8 +54,8 @@ requirements: - boost-cpp - qt-main >=5.15.8 - eigen >=3.3.4 - - python {{ python }} - - numpy {{ numpy }} + - python >=3.9,<3.13 + - numpy >=1.23.* - pandas - matplotlib-base - sysroot_linux-64 =2.17 # [linux] diff --git a/recipes/quast/meta.yaml b/recipes/quast/meta.yaml index 4b9f0a96c8548..bbe2024660d3b 100644 --- a/recipes/quast/meta.yaml +++ b/recipes/quast/meta.yaml @@ -1,12 +1,14 @@ -{% set version = "5.2.0" %} -{% set hash = "ccd911087cfa254ad4b8eadac4f95d4685e44c3996f5516b8e0ce6f7cfa7e0db" %} +{% set version = "5.3.0" %} +{% set hash = "ac9dba03ef9d0a51d7a9e2c56826104e78f340f6263a3ad393648442debc74ec" %} package: name: quast version: {{ version }} build: - number: 4 + number: 0 + run_exports: + - {{ pin_subpackage("quast", max_pin="x.x") }} source: url: diff --git a/recipes/r-oncopharmadb/meta.yaml b/recipes/r-oncopharmadb/meta.yaml index 999f9600bc26a..963fd3894e35a 100644 --- a/recipes/r-oncopharmadb/meta.yaml +++ b/recipes/r-oncopharmadb/meta.yaml @@ -1,5 +1,5 @@ {% set name = "r-oncopharmadb" %} -{% set version = "1.7.0" %} +{% set version = "1.8.1" %} {% set github = "https://github.com/sigven/oncoPharmaDB" %} package: @@ -8,7 +8,7 @@ package: source: url: https://github.com/sigven/pharmOncoX/archive/refs/tags/{{ version }}.tar.gz - sha256: 001e9b133028b00df90fa7081ad315fcb28be671ac7477cf6b689f0e0ca539fb + sha256: e21386183a6916c328dac32e0ea92a5d9c1d28921b4e3e14d4b63515335a1f51 build: number: 0 diff --git a/recipes/r-quilt/meta.yaml b/recipes/r-quilt/meta.yaml index b18e2ef0e20cd..6e6ef9613842c 100644 --- a/recipes/r-quilt/meta.yaml +++ b/recipes/r-quilt/meta.yaml @@ -1,6 +1,6 @@ {% set name = "r-quilt" %} -{% set version = "2.0.0" %} -{% set sha256 = "723c52371fd8c495a54165b168db70d8c4ce001cd4dc902e63db0240318e8a6e" %} +{% set version = "2.0.1" %} +{% set sha256 = "6e0f041641c96014b879a7fea6c0cc21351a83e8ba938c828c07a0c297574eba" %} package: name: '{{ name }}' @@ -11,7 +11,7 @@ source: sha256: '{{ sha256 }}' build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('r-quilt', max_pin="x") }} diff --git a/recipes/r-remapenrich/build.sh b/recipes/r-remapenrich/build.sh new file mode 100644 index 0000000000000..df943f40e3e3d --- /dev/null +++ b/recipes/r-remapenrich/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# 'Autobrew' is being used by more and more packages these days +# to grab static libraries from Homebrew bottles. These bottles +# are fetched via Homebrew's --force-bottle option which grabs +# a bottle for the build machine which may not be macOS 10.9. +# Also, we want to use conda packages (and shared libraries) for +# these 'system' dependencies. See: +# https://github.com/jeroen/autobrew/issues/3 +export DISABLE_AUTOBREW=1 + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${R} CMD INSTALL --build . ${R_ARGS} + +# Add more build steps here, if they are necessary. + +# See +# https://docs.conda.io/projects/conda-build +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-remapenrich/meta.yaml b/recipes/r-remapenrich/meta.yaml new file mode 100644 index 0000000000000..4d73492800c64 --- /dev/null +++ b/recipes/r-remapenrich/meta.yaml @@ -0,0 +1,86 @@ +{% set version = '0.99.0' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-remapenrich + version: {{ version|replace("-", "_") }} + +source: + url: https://github.com/nigiord/ReMapEnrich/archive/refs/tags/v{{ version }}.tar.gz + sha256: 87764400fbe3fbb41fda2395b669c9e926f7e39323a590f53f2944a9cd720aaf + +build: + noarch: generic + merge_build_host: True # [win] + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + run_exports: + - {{ pin_subpackage('r-remapenrich', max_pin='x.x') }} + +# Suggests: knitr, rmarkdown +requirements: + build: + - {{ posix }}filesystem # [win] + - {{ posix }}git + - {{ posix }}zip # [win] + + host: + - r-base >=3.3 + - bioconductor-genomicranges + - r-r.utils + - r-rmysql + - r-data.table + + run: + - r-base >=3.3 + - bioconductor-genomicranges + - r-r.utils + - r-rmysql + - r-data.table + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('ReMapEnrich')" # [not win] + - "\"%R%\" -e \"library('ReMapEnrich')\"" # [win] + + # You can also put a file called run_test.py, run_test.sh, or run_test.bat + # in the recipe that will be run at test time. + + # requires: + # Put any additional test requirements here. + +about: + home: https://github.com/nigiord/ReMapEnrich + license: AGPL-3 + summary: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap + peaks + license_family: AGPL + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/AGPL-3' + +extra: + recipe-maintainers: + - nigiord + +# The original CRAN metadata for this package was: + +# Package: ReMapEnrich +# Title: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks +# Version: 0.99.0 +# Authors@R: c(person("Zacharie", "Menetrier", email = "zacharie.menetrier@gmail.com", role = c("aut", "cre")), person("Martin", "Mestdagh", email = "martin.mestdagh@gmail.com", role = c("aut"))) +# Description: Bioinformatics tools to compute statistical enrichment of geonomic regions for ReMap peaks +# Depends: R (>= 3.3), GenomicRanges, data.table, R.utils, RMySQL +# LazyData: true +# RoxygenNote: 6.1.1 +# License: GNU Affero General Public License +# Suggests: knitr, rmarkdown +# VignetteBuilder: knitr +# biocViews: c("GeneExpression", "GeneSetEnrichment", "GenomeAnnotation", "Software") + +# See +# https://docs.conda.io/projects/conda-build for +# more information about meta.yaml diff --git a/recipes/r-seamless/meta.yaml b/recipes/r-seamless/meta.yaml index 7ab85b48ac9dd..bc06815b02ea7 100644 --- a/recipes/r-seamless/meta.yaml +++ b/recipes/r-seamless/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.1.0' %} +{% set version = '0.1.1' %} package: name: r-seamless @@ -8,14 +8,16 @@ source: url: - {{ cran_mirror }}/src/contrib/seAMLess_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/seAMLess/seAMLess_{{ version }}.tar.gz - sha256: ab737087b3341884e915530d772948130f60299a65af40c43e101a8c819a37a3 + sha256: 8bba2ae29cd9b92fad6e5a1b12aed589ee10b49ef81189524236b07d994ea07b build: - number: 3 + number: 0 noarch: generic rpaths: - lib/R/lib/ - lib/ + run_exports: + - {{ pin_subpackage("r-seamless", max_pin="x.x") }} requirements: host: @@ -25,6 +27,7 @@ requirements: - r-ggtern - r-randomforest - r-music + - r-optparse run: - r-base - bioconductor-biobase @@ -33,6 +36,7 @@ requirements: - r-randomforest - r-music - xbioc + - r-optparse test: commands: diff --git a/recipes/regenie/meta.yaml b/recipes/regenie/meta.yaml index e61e5e7317c02..71895d3fa8aa6 100644 --- a/recipes/regenie/meta.yaml +++ b/recipes/regenie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "regenie" %} -{% set version = "3.6" %} -{% set sha256 = "bb935b196da08ef7b37dad9736022030a686ae84539c47c106de6096d4612e09" %} +{% set version = "4.0" %} +{% set sha256 = "8f678d55bccf18ab70680637aca3cfd737060b3da291c803f3016d2ac3a07ccf" %} package: name: {{ name|lower }} diff --git a/recipes/reseek/meta.yaml b/recipes/reseek/meta.yaml index 334df5bf224a4..8b59a2d8fb690 100644 --- a/recipes/reseek/meta.yaml +++ b/recipes/reseek/meta.yaml @@ -1,5 +1,5 @@ {% set name = "reseek" %} -{% set version = "2.0.1" %} +{% set version = "2.02" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/rcedgar/reseek/archive/refs/tags/v{{ version }}.tar.gz - sha256: 79a2aca249547a164ff7a6460abc6875c182a40693ac07068cc859b7cb7a95ec + sha256: 83296e5edcdccdf4848f52ff34f35b753fa9ae1d383c3347eee41ef7d26888b1 build: number: 0 diff --git a/recipes/resistify/meta.yaml b/recipes/resistify/meta.yaml index 47f4980eaa8d8..6a2defda2afbc 100644 --- a/recipes/resistify/meta.yaml +++ b/recipes/resistify/meta.yaml @@ -1,6 +1,6 @@ {% set name = "resistify" %} -{% set version = "0.5.1" %} -{% set sha256 = "d89d8d3553fd14c1ca4f6a7a995910a3244f1e70ccd06148be6c1278229183b5" %} +{% set version = "0.5.2" %} +{% set sha256 = "2c8e71e4ce52f014a62e5a5a5b32c04ed67af3651ddf9013f96953e711f4d234" %} package: name: "{{ name }}" @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 entry_points: - resistify = resistify.main:main script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv " diff --git a/recipes/rpsbproc/build.sh b/recipes/rpsbproc/build.sh index dbaea1d1ac5e7..a152fae34917c 100755 --- a/recipes/rpsbproc/build.sh +++ b/recipes/rpsbproc/build.sh @@ -125,9 +125,11 @@ CONFIGURE_FLAGS="$CONFIGURE_FLAGS --without-dll --with-static-exe" # Platform-specific flags if [[ "$(uname)" = "Linux" ]]; then # --with(out)-64: - # Compile in 64-bit mode instead of 32-bit. + # Compile in 64-bit mode instead of 32-bit on x86_64 platforms. # Flag not available for osx build. - CONFIGURE_FLAGS="$CONFIGURE_FLAGS --with-64" + if [[ "$(arch)" = "x86_64" ]]; then + CONFIGURE_FLAGS="$CONFIGURE_FLAGS --with-64" + fi # --with(out)-openmp: # Enable OpenMP extensions for all projects. # Does not work without hacks for OSX @@ -154,7 +156,7 @@ cd "$NCBI_CXX_TOOLKIT" # Run GNU Make cd "$RESULT_PATH/build" echo "RUNNING MAKE" >&2 -make -j1 -f Makefile.flat rpsbproc.exe >&2 +make -j 4 -f Makefile.flat rpsbproc.exe >&2 # Copy compiled binaries to the Conda $PREFIX mkdir -p "$PREFIX/bin" diff --git a/recipes/rpsbproc/meta.yaml b/recipes/rpsbproc/meta.yaml index e6f28433383b3..6f42c04bad539 100644 --- a/recipes/rpsbproc/meta.yaml +++ b/recipes/rpsbproc/meta.yaml @@ -24,7 +24,7 @@ source: - update_configsub.patch build: - number: 0 + number: 1 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} @@ -81,3 +81,7 @@ about: extra: identifiers: - doi:10.1002/cpbi.90 + additional-platforms: + - linux-aarch64 + # osx-arm64 is encountering issues with Xcode and make during builds + # - osx-arm64 diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml index 881bc4b84bda7..5dd7db2b51e4d 100644 --- a/recipes/saccharis/meta.yaml +++ b/recipes/saccharis/meta.yaml @@ -1,6 +1,6 @@ {% set name = "SACCHARIS" %} {% set version = "2.0.1.dev21" %} -{% set hash = "551DE1D7B666A5AD693DD61F58A2617BAB3F708836D0143A7FBB981365F45AF4" %} +{% set hash = "DEFE4B98CFF4F5ED58A102D7FFE0CC219C4EC44C257AC0469255CDC73F124F57" %} package: @@ -9,12 +9,12 @@ package: source: # url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz - url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_5.tar.gz + url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_7.tar.gz sha256: {{ hash|lower }} build: noarch: python - number: 5 + number: 7 script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt preserve_egg_dir: True # added because the entry points below seem to be causing a build error @@ -37,7 +37,7 @@ requirements: - python - setuptools host: - - python >=3.6 + - python >=3.11 - setuptools - pip run: @@ -53,7 +53,7 @@ requirements: - modeltest-ng >=0.1.7 # [not win] - muscle >=3.8 # [not win] - psutil - - python >=3.8 + - python >=3.11 - python-dotenv >=0.20.0 - raxml >=8.2.12 # [not win] - raxml-ng >=1.2 # [not win] diff --git a/recipes/savana/meta.yaml b/recipes/savana/meta.yaml index f9c03bb28ca14..30c1107c415c2 100644 --- a/recipes/savana/meta.yaml +++ b/recipes/savana/meta.yaml @@ -1,5 +1,5 @@ {% set name = "savana" %} -{% set version = "1.2.3" %} +{% set version = "1.2.4" %} package: name: "{{ name }}" @@ -7,7 +7,7 @@ package: source: url: "https://github.com/cortes-ciriano-lab/{{ name }}/archive/{{ version }}.tar.gz" - sha256: 3d7b7258b59b7f8bc2704eed131df81db77931f790c86b7af19100554fa9d44f + sha256: 3d9f341259a41a964341fad1ce08f1a58d980bc75d2659181c6d41f8acc68204 build: number: 0 diff --git a/recipes/seqspec/meta.yaml b/recipes/seqspec/meta.yaml index c4a928dfcb61f..60296907ebdc4 100644 --- a/recipes/seqspec/meta.yaml +++ b/recipes/seqspec/meta.yaml @@ -1,5 +1,5 @@ {% set name = "seqspec" %} -{% set version = "0.3.0" %} +{% set version = "0.3.1" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/seqspec-{{ version }}.tar.gz - sha256: d9e6c283daaca06f58f1090c0c7dcfecf646b9658e62aa873a4e85fef56c56c9 + sha256: 1c71201e3913526542f4fe7dfcbc866a295976e983dc91c7f53efb655797b3c2 build: run_exports: diff --git a/recipes/sigprofilermatrixgenerator/meta.yaml b/recipes/sigprofilermatrixgenerator/meta.yaml index a1960b918d439..a1774cd036abe 100644 --- a/recipes/sigprofilermatrixgenerator/meta.yaml +++ b/recipes/sigprofilermatrixgenerator/meta.yaml @@ -1,5 +1,5 @@ {% set name = "SigProfilerMatrixGenerator" %} -{% set version = "1.2.30" %} +{% set version = "1.2.31" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/SigProfilerMatrixGenerator-{{ version }}.tar.gz - sha256: 55453304c565acacc62bce77592f8c44a14bca367df33585825f06893e315280 + sha256: 632621178fc6c572d0953c24bff7a1079e55311ea870ee02ecb90468a894a5d2 build: entry_points: diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 5130d754bac38..700e7526b5919 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.11.1" %} +{% set version = "0.11.2" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 293a951dcf829400bf6197705d6c602faed95aaaae9ad0d661d23b0184074134 + sha256: fca29038d78387c237afb4ec2b04638e6128d2456940dd7b96ac4205f319d7f3 build: noarch: python diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index 5ef003764825c..417adf4f21c71 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,7 +1,7 @@ # Attention: when upgrading the version, please compare below dependencies with # https://github.com/snakemake/snakemake/blob/{version}/setup.cfg {% set name = "snakemake" %} -{% set version = "8.25.1" %} +{% set version = "8.25.3" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: url: https://pypi.io/packages/source/s/{{ name }}/snakemake-{{ version }}.tar.gz - sha256: c8f4442473f3af130f237fe5759ebfb03997b44e713cd7c479aba27d71338cd9 + sha256: b05262fbb25b8b463ea45f92789c39935a775c02b072be8a42e6cd262ed86c21 build: number: 0 diff --git a/recipes/snapatac2/build.sh b/recipes/snapatac2/build.sh index 3f270cc862d95..b9259f5b409d3 100644 --- a/recipes/snapatac2/build.sh +++ b/recipes/snapatac2/build.sh @@ -6,6 +6,6 @@ RUST_BACKTRACE=1 maturin build -m snapatac2-python/Cargo.toml -b pyo3 --interpreter "${PYTHON}" --release --strip # Install *.whl files using pip -${PYTHON} -m pip install snapatac2-python/target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv +${PYTHON} -m pip install target/wheels/*.whl --no-deps --no-build-isolation --no-cache-dir -vvv cd ${SRC_DIR}/snapatac2-python/ && cargo clean && rm -rf ${BUILD_PREFIX}/.cargo diff --git a/recipes/snapatac2/meta.yaml b/recipes/snapatac2/meta.yaml index ace1bae3532d1..04b6501a2c45d 100644 --- a/recipes/snapatac2/meta.yaml +++ b/recipes/snapatac2/meta.yaml @@ -1,13 +1,13 @@ {% set name = "snapatac2" %} -{% set version = "2.7.0" %} -{% set sha256 = "a37e86001da1e8f812d2e2dfda157ce131b8a0b54a44ae5bd72733c0171d4f1d" %} +{% set version = "2.7.1" %} +{% set sha256 = "18c206153112fbf9ca97c690d6d8d1e51cb5d125739ead6e8a3aece8f01cbd66" %} package: name: {{ name }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snapatac2-{{ version }}.tar.gz + url: https://github.com/kaizhang/SnapATAC2/archive/refs/tags/v{{ version }}.tar.gz sha256: {{ sha256 }} patches: - cargo.toml.patch @@ -50,6 +50,7 @@ requirements: - scikit-learn >=1.0 - tqdm >=4.62 - typing_extensions + - typeguard >=4.0 test: imports: @@ -60,7 +61,7 @@ about: summary: "SnapATAC2: Single-cell epigenomics analysis pipeline." license: MIT license_family: MIT - license_file: LICENSE + license_file: snapatac2-python/LICENSE doc_url: "https://kzhang.org/SnapATAC2" dev_url: "https://github.com/kaizhang/SnapATAC2" diff --git a/recipes/snapatac2/pyproject.toml.patch b/recipes/snapatac2/pyproject.toml.patch index 1c87870e9049d..920d2e5eb30fb 100644 --- a/recipes/snapatac2/pyproject.toml.patch +++ b/recipes/snapatac2/pyproject.toml.patch @@ -1,14 +1,13 @@ -diff --git a/pyproject.toml b/pyproject.toml -index 0cc0ca0..eeb5899 100644 ---- a/pyproject.toml -+++ b/pyproject.toml -@@ -7,6 +7,9 @@ features = ["pyo3/extension-module"] +diff --git a/snapatac2-python/pyproject.toml b/snapatac2-python/pyproject.toml +index 15d7b75..82f9c43 100644 +--- a/snapatac2-python/pyproject.toml ++++ b/snapatac2-python/pyproject.toml +@@ -6,6 +6,8 @@ build-backend = "maturin" + features = ["pyo3/extension-module"] python-source = "python" module-name = "snapatac2._snapatac2" - manifest-path = "snapatac2-python/Cargo.toml" +strip = true +profile = "release" -+locked = true [project] name = "snapatac2" diff --git a/recipes/sniffles/meta.yaml b/recipes/sniffles/meta.yaml index 445120497e1c0..bf2b788e117fb 100644 --- a/recipes/sniffles/meta.yaml +++ b/recipes/sniffles/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.4" %} -{% set sha256 = "e3c2f552105cd5f5941d6291b9ee9dbfe634ad19b5e7a64fa26b9e2daa6547d4" %} +{% set version = "2.5.2" %} +{% set sha256 = "b041580091a87d8c180303a1cb8ca513864ad1b41e64928fc0e04a59fdf5a80f" %} package: name: sniffles @@ -12,18 +12,18 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - {{ pin_subpackage('sniffles', max_pin="x") }} requirements: host: - - python >=3.10 + - python ==3.10.15 - pip run: - - python >=3.10 + - python ==3.10.15 - pysam >=0.21.0 - - edlib >=1.3.9 + - python-edlib >=1.3.9 - psutil >=5.9.4 test: @@ -31,11 +31,18 @@ test: - sniffles --help about: - home: https://github.com/fritzsedlazeck/Sniffles + home: "https://github.com/fritzsedlazeck/Sniffles" license: MIT license_file: LICENSE license_family: MIT - summary: Sniffles is a structural variation caller using third generation sequencing - (PacBio or Oxford Nanopore) - doc_url: https://github.com/fritzsedlazeck/Sniffles/wiki - dev_url: https://github.com/fritzsedlazeck/Sniffles + summary: "Sniffles is a structural variation caller using third generation sequencing + (PacBio or Oxford Nanopore)." + doc_url: "https://github.com/fritzsedlazeck/Sniffles/wiki" + dev_url: "https://github.com/fritzsedlazeck/Sniffles" + +extra: + identifiers: + - doi:10.1038/s41587-023-02024-y + - doi:10.1038/s41592-018-0001-7 + - biotools:sniffles + - usegalaxy-eu:sniffles diff --git a/recipes/snipe/meta.yaml b/recipes/snipe/meta.yaml index cdd65fa2609dc..a5b3dfc5fc2b5 100644 --- a/recipes/snipe/meta.yaml +++ b/recipes/snipe/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snipe" %} -{% set version = "0.1.5" %} +{% set version = "0.1.6" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/snipe-bio/snipe/archive/refs/tags/v{{ version }}.tar.gz - sha256: 70fbf5dddc7e843cf5a2225e66423e4842c21757b7d8646542913aa2cddbf1b6 + sha256: 6847a51dbfca18442681f7981483401741a9860c0399f3f2592bb3894227afb8 build: number: 0 diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml index 6b95c234d852a..b1f2a2bcc8252 100644 --- a/recipes/squirrel/meta.yaml +++ b/recipes/squirrel/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.11" %} +{% set version = "1.0.12" %} {% set name = "squirrel" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz - sha256: 2d3a4e1a3227372f32ffb6d97005efb08839b53e71f1b6e3d844fe8327835fe5 + sha256: a99eb37903d553c0bee2f2e0bc5104035fac6644f3115a7986619abf6a29297c build: number: 0 diff --git a/recipes/strainge/build_failure.linux-64.yaml b/recipes/strainge/build_failure.linux-64.yaml deleted file mode 100644 index aff92ef2abc4c..0000000000000 --- a/recipes/strainge/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8d421a84b249ede354ec5b8b84c06165e973405ca4cf7997724b3633e681d5b8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - - [1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip. - [1;35mfull command[0m: [34m/opt/conda/conda-bld/strainge_1717901108313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python /opt/conda/conda-bld/strainge_1717901108313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmps55ogjs_[0m - [1;35mcwd[0m: /opt/conda/conda-bld/strainge_1717901108313/work - Preparing metadata (pyproject.toml): finished with status 'error' - [1;31merror[0m: [1mmetadata-generation-failed[0m - - [31m[0m Encountered error while generating package metadata. - [31m>[0m See above for output. - - [1;35mnote[0m: This is an issue with the package mentioned above, not pip. - [1;36mhint[0m: See above for details. - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata - distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel - return super().prepare_metadata_for_build_wheel( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel - return self._call_hook('prepare_metadata_for_build_wheel', { - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook - self._subprocess_runner( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner - call_subprocess( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess - raise error - pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run - requirement_set = resolver.resolve( - ^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve - collected = self.factory.collect_root_requirements(root_reqs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements - reqs = list( - ^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req - cand = self._make_base_candidate_from_link( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link - self._link_candidate_cache[link] = LinkCandidate( - ^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ - super().__init__( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ - self.dist = self._prepare() - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare - dist = self._prepare_distribution() - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution - return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement - return self._prepare_linked_requirement(req, parallel_builds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement - dist = _get_prepared_distribution( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution - abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata - self.req.prepare_metadata() - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata - self.metadata_directory = generate_metadata( - ^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata - raise MetadataGenerationFailed(package_details=details) from error - pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/tmp/pip-build-tracker-dk_u9tdk' - Removed build tracker: '/tmp/pip-build-tracker-dk_u9tdk' - Traceback (most recent call last): - File "/opt/conda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/strainge_1717901108313/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/strainge/build_failure.osx-64.yaml b/recipes/strainge/build_failure.osx-64.yaml deleted file mode 100644 index 16a4be15fc58e..0000000000000 --- a/recipes/strainge/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 8d421a84b249ede354ec5b8b84c06165e973405ca4cf7997724b3633e681d5b8 # The hash of the recipe's meta.yaml at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strainge-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/strainge-1.3.8 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-ka0pkz1f - Initialized build tracking at /private/tmp/pip-build-tracker-ka0pkz1f - Created build tracker: /private/tmp/pip-build-tracker-ka0pkz1f - Entered build tracker: /private/tmp/pip-build-tracker-ka0pkz1f - Created temporary directory: /private/tmp/pip-install-y6nw1c6k - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-vyuojn_m - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-ka0pkz1f' - Created temporary directory: /private/tmp/pip-modern-metadata-tvd9hhrw - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'error' - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata - distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/misc.py", line 766, in prepare_metadata_for_build_wheel - return super().prepare_metadata_for_build_wheel( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel - return self._call_hook('prepare_metadata_for_build_wheel', { - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook - self._subprocess_runner( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 252, in runner - call_subprocess( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess - raise error - pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 - - The above exception was the direct cause of the following exception: - - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 377, in run - requirement_set = resolver.resolve( - ^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 76, in resolve - collected = self.factory.collect_root_requirements(root_reqs) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 534, in collect_root_requirements - reqs = list( - ^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 490, in _make_requirements_from_install_req - cand = self._make_base_candidate_from_link( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/factory.py", line 228, in _make_base_candidate_from_link - self._link_candidate_cache[link] = LinkCandidate( - ^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 290, in __init__ - super().__init__( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ - self.dist = self._prepare() - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 222, in _prepare - dist = self._prepare_distribution() - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 301, in _prepare_distribution - return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 525, in prepare_linked_requirement - return self._prepare_linked_requirement(req, parallel_builds) - ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 640, in _prepare_linked_requirement - dist = _get_prepared_distribution( - ^^^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution - abstract_dist.prepare_distribution_metadata( - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/distributions/sdist.py", line 67, in prepare_distribution_metadata - self.req.prepare_metadata() - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/req/req_install.py", line 579, in prepare_metadata - self.metadata_directory = generate_metadata( - ^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata - raise MetadataGenerationFailed(package_details=details) from error - pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed - Removed file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-ka0pkz1f' - Removed build tracker: '/private/tmp/pip-build-tracker-ka0pkz1f' -# Last 100 lines of the build log. diff --git a/recipes/strainge/meta.yaml b/recipes/strainge/meta.yaml index 87bd9aeccfa3d..c89ccefaae546 100644 --- a/recipes/strainge/meta.yaml +++ b/recipes/strainge/meta.yaml @@ -1,5 +1,5 @@ {% set name = "strainge" %} -{% set version = "1.3.8" %} +{% set version = "1.3.9" %} package: name: "{{ name|lower }}" @@ -7,16 +7,16 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d93f1d5fea0f13519cdf19e6b0914c8ef5ce07778d653b74db267e92643e4bd1 + sha256: a056798fdadf9cb9d12675cb421508c0605e637f4a5baf468eca32922ed30d08 build: - number: 1 - skip: true # [py<38] + number: 0 + skip: True # [py < 38] entry_points: - strainge=strainge.cli.main:strainge_cli - straingst=strainge.cli.main:straingst_cli - straingr=strainge.cli.main:straingr_cli - script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + script: {{ PYTHON }} -m pip install . --no-build-isolation --no-cache-dir --no-deps -vvv run_exports: - {{ pin_subpackage("strainge", max_pin="x") }} @@ -28,11 +28,12 @@ requirements: - pip - pybind11 >=2.2 - numpy + - toml + - versioneer - zlib run: - python - - numpy - - pybind11 >=2.2 + - {{ pin_compatible('numpy') }} - h5py - intervaltree - matplotlib-base @@ -57,6 +58,7 @@ about: license_family: BSD license_file: LICENSE summary: "Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains." + dev_url: https://github.com/broadinstitute/strainge extra: recipe-maintainers: diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml index 02668243ae353..9590c0f9fee59 100644 --- a/recipes/strangepg/meta.yaml +++ b/recipes/strangepg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "strangepg" %} -{% set version = "0.8.12" %} +{% set version = "0.8.13" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 323c161f3be6ec3c2d43cc7daeb7b139f75fb4ed70ec095f22e39d2450dd912c + sha256: b7dc45385297fa46458bf83931acd7dbc0fdbb594f63fe59db12d9a5080a95d8 build: number: 0 diff --git a/recipes/sylph/build.sh b/recipes/sylph/build.sh index 3662f6efb60db..bdab29de4ab9e 100644 --- a/recipes/sylph/build.sh +++ b/recipes/sylph/build.sh @@ -1,8 +1,4 @@ #!/bin/bash -euo -# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. -# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. -export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" - # build statically linked binary with Rust RUST_BACKTRACE=1 cargo install --verbose --path . --root $PREFIX diff --git a/recipes/sylph/meta.yaml b/recipes/sylph/meta.yaml index 06ecabc04a199..b6e2318d12140 100644 --- a/recipes/sylph/meta.yaml +++ b/recipes/sylph/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.6.1" %} +{% set version = "0.7.0" %} package: name: sylph @@ -11,12 +11,12 @@ build: source: url: https://github.com/bluenote-1577/sylph/archive/v{{ version }}.tar.gz - sha256: 9f384ecf33d5eed57e518c1cc238ffb5ac68948dcf921731ba77ccbd02b57bdb + sha256: 8d0dd0c4b64de9b4c7402f6a44a019b2f54aae0626308a6b8831b3239640b609 requirements: build: - {{ compiler("cxx") }} - - rust >=1.61 + - {{ compiler("rust") }} - make - cmake >=3.12 @@ -27,10 +27,11 @@ test: about: home: https://github.com/bluenote-1577/sylph license: MIT + license_family: MIT summary: sylph quickly enables querying of genomes against even low-coverage shotgun metagenomes to find nearest neighbour ANI. license_file: LICENSE + dev_url: https://github.com/bluenote-1577/sylph extra: recipe-maintainers: - bluenote-1577 - diff --git a/recipes/table2asn/build.sh b/recipes/table2asn/build.sh index 6e0c82f01b182..3e7c35737880e 100644 --- a/recipes/table2asn/build.sh +++ b/recipes/table2asn/build.sh @@ -3,10 +3,10 @@ gunzip *table2asn.gz mkdir -p ${PREFIX}/bin -if [ `uname` == Darwin ]; then - cp mac.table2asn ${PREFIX}/bin/table2asn +if [[ `uname` == Darwin ]]; then + cp -f mac.table2asn ${PREFIX}/bin/table2asn else - cp *.table2asn ${PREFIX}/bin/table2asn + cp -f *.table2asn ${PREFIX}/bin/table2asn fi chmod 0755 "${PREFIX}/bin/table2asn" @@ -15,7 +15,7 @@ chmod 0755 "${PREFIX}/bin/table2asn" # patchelf to modify the RPATH of table2asn's libbz libraries; refer to: # https://github.com/bioconda/bioconda-recipes/pull/38770#issuecomment-1473627378 -if [ `uname` == Darwin ]; then +if [[ `uname` == Darwin ]]; then install_name_tool -change libbz2.1.dylib libbz2.1.0.dylib "${PREFIX}/bin/table2asn" install_name_tool -add_rpath "${PREFIX}/lib" "${PREFIX}/bin/table2asn" else diff --git a/recipes/table2asn/meta.yaml b/recipes/table2asn/meta.yaml index 9787dc6a10cc7..b337b71f5de5c 100644 --- a/recipes/table2asn/meta.yaml +++ b/recipes/table2asn/meta.yaml @@ -1,7 +1,7 @@ {% set name = "table2asn" %} -{% set version = "1.28.1111" %} -{% set sha256 = "626116210fea6b1426092e370c32c7f766a6cc98857c4202712eb7b265da23cb" %} -{% set release_date = "2024-06-18" %} +{% set version = "1.28.1179" %} +{% set sha256 = "7cdb95ccd7e025a54ad093f00c7d63f95ad2a4b0b433287657cb6a45e5125be7" %} +{% set release_date = "2024-10-23" %} package: name: {{ name }} @@ -9,7 +9,7 @@ package: source: - url: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/{{ release_date }}/by_program/{{ name }}/mac.{{ name }}.gz # [osx] - sha256: 1b3ce05a1d3ef5afaa38c9b5c5a520b74d27aea9b516513ec647576e3a98bb32 # [osx] + sha256: ccb439c328f40ef82dae12f84a5ad4f0ccd442b7e8dbef83bcbebe81efb85781 # [osx] - url: https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/{{ release_date }}/by_program/{{ name }}/linux64.{{ name }}.gz # [linux] sha256: {{ sha256 }} # [linux] diff --git a/recipes/thapbi-pict/meta.yaml b/recipes/thapbi-pict/meta.yaml index 1451e942c5aca..1d9c74e0bf53f 100644 --- a/recipes/thapbi-pict/meta.yaml +++ b/recipes/thapbi-pict/meta.yaml @@ -1,5 +1,5 @@ {% set name = "thapbi-pict" %} -{% set version = "1.0.16" %} +{% set version = "1.0.17" %} package: name: "{{ name|lower }}" @@ -7,33 +7,34 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name | replace("-", "_") }}/{{ name | replace("-", "_") }}-{{ version }}.tar.gz - sha256: 85cf6d180db38166bb7ccd14af8c3813e2b3fa0d5026cac76bce8867492563f7 + sha256: 030f27b94f5390de58f1e5b227d7fd1de50e7a6b01bb0fafd2b4320bee7c87f8 build: noarch: python number: 0 entry_points: - thapbi_pict = thapbi_pict.__main__: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" run_exports: - {{ pin_subpackage(name, max_pin="x") }} requirements: host: - pip - - python >=3.8 + - python >=3.10 + - setuptools run: # Python - biom-format >=2.1.14 - - biopython >=1.82 - - cutadapt >=4.0 - - matplotlib-base >=3.7 - - networkx >=2.4,!=2.8.3,!=2.8.4 - - pydot <3 - - python >=3.8 - - rapidfuzz >=2.4.0 - - sqlalchemy >=2.0 - - xlsxwriter + - biopython >=1.84 + - cutadapt >=4.9 + - matplotlib-base >=3.9.2 + - networkx >=3.4.2 + - pydot >=3.0.1 + - python >=3.10 + - rapidfuzz >=3.10.1 + - sqlalchemy >=2.0.36 + - xlsxwriter >=3.2 # Command line - blast - flash >=1.2.11 diff --git a/recipes/trtools/meta.yaml b/recipes/trtools/meta.yaml index cf9d3fb5e9a6f..8f4af88b5cc12 100644 --- a/recipes/trtools/meta.yaml +++ b/recipes/trtools/meta.yaml @@ -1,5 +1,5 @@ {% set name = "trtools" %} -{% set version = "6.0.2" %} +{% set version = "6.1.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 7bdb476951a4ec748df20058a31da3d1def14554cd9a67f85d3c61bf63f8f303 + sha256: 3a177cf19060945eff4044f16d5ebdc66364e72a8a3c9bd725086ba10003df96 build: noarch: python @@ -20,6 +20,7 @@ build: - associaTR=trtools.associaTR:run - prancSTR = trtools.prancSTR:run - simTR = trtools.simTR:run + - annotaTR = trtools.annotaTR:run script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" number: 0 run_exports: @@ -32,7 +33,7 @@ requirements: - pip >=20.3 run: - python >=3.7.1,<4.0 - - cyvcf2 >=0.30.4 + - cyvcf2 >=0.30.27 - matplotlib-base >=3.1.2 - numpy >=1.17.3 - pandas >=1.2.0 @@ -42,6 +43,7 @@ requirements: - statsmodels >=0.10.2 - pyfaidx >=0.5.6 - ART >=2016.06.05 + - pgenlib >=0.90.1 test: imports: @@ -54,6 +56,7 @@ test: - trtools.statSTR - trtools.prancSTR - trtools.simTR + - trtools.annotaTR - trtools.utils requires: - bcftools @@ -69,6 +72,7 @@ test: - qcSTR --help - prancSTR --help - simTR --help + - annotaTR --help about: home: https://github.com/gymreklab/TRTools @@ -86,3 +90,6 @@ extra: identifiers: - biotools:trtools - doi:10.1093/bioinformatics/btaa736 + additional-platforms: + - osx-arm64 + - linux-aarch64 diff --git a/recipes/varfish-cli/meta.yaml b/recipes/varfish-cli/meta.yaml index 6baa90f445ec8..4f0542b85b1b0 100644 --- a/recipes/varfish-cli/meta.yaml +++ b/recipes/varfish-cli/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.6.3" %} -{% set sha256 = "7a7344b3d88b8ac303f0a54f7709fa528fe1555dd6e935c45e6ec452d955871d" %} +{% set version = "0.6.4" %} +{% set sha256 = "229fbfb2798f5703fc2023b24034e05a6af7356681de0c0fa902f68fe80f1490" %} package: name: varfish-cli @@ -11,7 +11,7 @@ source: build: noarch: python - number: 2 + number: 0 script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv entry_points: - varfish-cli = varfish_cli.__main__:main @@ -22,6 +22,7 @@ requirements: host: - python >=3 - pip + - setuptools run: - python >=3.9 - attrs diff --git a/recipes/vg/meta.yaml b/recipes/vg/meta.yaml index 4500b2e91bddb..a9174ae4e5e91 100644 --- a/recipes/vg/meta.yaml +++ b/recipes/vg/meta.yaml @@ -1,5 +1,5 @@ {% set name = "vg" %} -{% set version = "1.60.0" %} +{% set version = "1.61.0" %} package: name: {{ name }} @@ -7,9 +7,9 @@ package: source: - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg # [linux and x86_64] - sha256: 8a014a89301fa3168b19adadfa23753dcfd4af3944493199028ec79c141da22e # [linux and x86_64] + sha256: dfdc9f14c70aa68f05dcfdb8a9938f235f89353ce0f88076fc29a4ad92c3c7cf # [linux and x86_64] - url: https://github.com/vgteam/vg/releases/download/v{{ version }}/vg-arm64 # [linux and aarch64] - sha256: b7700ac536cee961e0fe6bfd5cfd3b3f93844be47b45f21d67e0a0208fc01bc0 # [linux and aarch64] + sha256: 835bdb1354e45dc1ad7e991adda92a327da2e24a09f6e2a53cad3a926510a2ac # [linux and aarch64] build: number: 0 diff --git a/recipes/yacht/meta.yaml b/recipes/yacht/meta.yaml index c38a49f2cc743..2fc7c8f32250f 100644 --- a/recipes/yacht/meta.yaml +++ b/recipes/yacht/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.2.3" %} +{% set version = "1.3.0" %} package: name: yacht @@ -6,19 +6,22 @@ package: source: url: https://github.com/KoslickiLab/YACHT/releases/download/v{{ version }}/yacht-{{ version }}.tar.gz - sha256: 93adb23ad4f143d48c9f0ea661fe2283ff42e9c51e073a05460596ecabc65214 + sha256: 68d272daeb70ed7390aa2d468934dc4bf0aa9a021f99fe99847b8a664e8ac8cf build: number: 0 - noarch: python - skip: True # [win or osx] - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + skip: True # [osx] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" run_exports: - - {{ pin_subpackage('yacht', max_pin="x") }} + - {{ pin_subpackage('yacht') }} requirements: + build: + - {{ compiler('cxx') }} + - make # Ensures that Make is available (for Unix) + host: - - python >3.6 + - python >3.6,<3.12 - pip - pandas - pytaxonkit @@ -27,16 +30,16 @@ requirements: - loguru - tqdm - biom-format - - numpy + - numpy >=1.22.4 - setuptools - requests + run: - - python >3.6 + - python >3.6,<3.12 - sourmash >=4.8.3,<5 - - rust - scipy - requests - - numpy + - numpy >=1.22.4 - pandas - scikit-learn - codecov @@ -51,7 +54,6 @@ requirements: - ruff - sourmash_plugin_branchwater - test: commands: - yacht --help @@ -67,19 +69,20 @@ about: extra: skip-lints: - - should_not_be_noarch_skip - should_use_compilers + - should_be_noarch_generic identifiers: - - doi:10.1101/2023.04.18.537298 + - doi:10.1093/bioinformatics/btae047 recipe-maintainers: + - chunyuma - dkoslicki authors: - dkoslicki - chunyuma + - mahmudhera - sew347 - mlupei - mfl15 - ShaopengLiu1 - raquellewei - mohsenht - diff --git a/recipes/zdb/meta.yaml b/recipes/zdb/meta.yaml index cdfd987fa4d37..11a5536b94524 100644 --- a/recipes/zdb/meta.yaml +++ b/recipes/zdb/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.3.3" %} +{% set version = "1.3.4" %} package: name: zdb @@ -11,8 +11,8 @@ build: - {{ pin_subpackage('zdb', max_pin="x.x") }} source: - url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.3.tar.gz - sha256: 9f5e29d3730740c2e60fb275db709916ef54d3a2c3e4cf54ae448e9add14bb49 + url: https://github.com/metagenlab/zDB/archive/refs/tags/v1.3.4.tar.gz + sha256: 6b9bb6433c05a1343794cc17e274dd58d202cc3a14a7f87b159fd381a8890e61 requirements: run: diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml index 328a669203374..b6bfbab475b0a 100644 --- a/recipes/zol/meta.yaml +++ b/recipes/zol/meta.yaml @@ -1,5 +1,5 @@ {% set name = "zol" %} -{% set version = "1.5.1" %} +{% set version = "1.5.2" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz - sha256: fdfd608d78bb62bb3068f6bfdbddfe850c4c2ed90b3ffd6d7817379faa01976d + sha256: 2e42064bacad5a6bd1b3d22fbdd2bb5f150b2e6aa0beb656794579ae7c9f6079 build: - number: 1 + number: 0 skip: True # [py != 310] run_exports: - {{ pin_subpackage('zol', max_pin='x') }} @@ -59,6 +59,8 @@ requirements: - codoff - gravis - colour + - rich-argparse + - tqdm test: commands: