diff --git a/biology/Makefile b/biology/Makefile index 6f35c5481dc7..11fc752f7b4c 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,256 +1,257 @@ COMMENT = Biology SUBDIR += R-cran-Biobase SUBDIR += R-cran-BiocGenerics SUBDIR += R-cran-BiocManager SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += atac-seq SUBDIR += augustus SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bamutil SUBDIR += barrnap SUBDIR += bbmap SUBDIR += bcf-score SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bifrost SUBDIR += bio-mocha SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += biolibc-tools SUBDIR += bioparser SUBDIR += biosig SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += btllib SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += chip-seq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasda SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gffread SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += kmcp SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libcombine SUBDIR += libgff SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += locarna SUBDIR += mafft SUBDIR += mapm3 SUBDIR += mashmap SUBDIR += megahit SUBDIR += metaeuk SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-PySCeS SUBDIR += py-bcbio-gff SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-biosig SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-deeptools SUBDIR += py-deeptoolsintervals SUBDIR += py-dna-features-viewer SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-htseq SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 + SUBDIR += py-macs3 SUBDIR += py-mrcfile SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pyfaidx SUBDIR += py-pyrodigal SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-valerius SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += salmon SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += seqwish SUBDIR += sigviewer SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wfa2-lib SUBDIR += wise .include diff --git a/biology/py-macs3/Makefile b/biology/py-macs3/Makefile new file mode 100644 index 000000000000..d2cad2892df4 --- /dev/null +++ b/biology/py-macs3/Makefile @@ -0,0 +1,49 @@ +PORTNAME= MACS3 +DISTVERSIONPREFIX= v +DISTVERSION= 3.0.0 +CATEGORIES= biology python +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Peak caller aimed at transcription factor binding sites +WWW= https://github.com/taoliu/MACS + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} \ + ${PYNUMPY} \ + simde>0:devel/simde \ + ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} +RUN_DEPENDS= ${PYNUMPY} \ + ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}hmmlearn>0:math/py-hmmlearn@${PY_FLAVOR} +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ + bash:shells/bash + +USES= localbase perl5 python shebangfix +USE_GITHUB= yes +USE_PERL5= test +USE_PYTHON= autoplist concurrent cython pep517 + +GH_ACCOUNT= macs3-project +GH_PROJECT= MACS +SHEBANG_FILES= test/cmdlinetest* test/prockreport test/*.py test/pyprofile* + +.include + +.if ${OPSYS} == FreeBSD && ${OSVERSION} < 1302509 +IGNORE= does not run properly on FreeBSD 13.2 and earlier due to use of dynamically loaded libc by py-threadpoolctl. Please upgrade to a newer FreeBSD or use py-macs2 instead. See PR 276231 +.endif + +post-stage: + ${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS3/*/*.so + +# FIXME: Some tests fail due to a py-threadpoolctl issue +# https://github.com/joblib/threadpoolctl/pull/148 +do-test: deinstall install + @${RM} -rf ${WRKSRC}/temp + @cd ${WRKSRC}/test && ./cmdlinetest tag + +.include diff --git a/biology/py-macs3/distinfo b/biology/py-macs3/distinfo new file mode 100644 index 000000000000..757e9bbaf640 --- /dev/null +++ b/biology/py-macs3/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1703890666 +SHA256 (macs3-project-MACS-v3.0.0_GH0.tar.gz) = faa7ec2ea1f47b8c4cd747f00f2754d0e40051fe44d81d229d0111e3dad34a1d +SIZE (macs3-project-MACS-v3.0.0_GH0.tar.gz) = 197389439 diff --git a/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c new file mode 100644 index 000000000000..d66d83f33606 --- /dev/null +++ b/biology/py-macs3/files/patch-MACS3_fermi-lite_ksw.c @@ -0,0 +1,11 @@ +--- MACS3/fermi-lite/ksw.c.orig 2023-11-15 16:09:23 UTC ++++ MACS3/fermi-lite/ksw.c +@@ -28,7 +28,7 @@ + + /* I modified this according to https://github.com/lh3/bwa/pull/283/*/ + #ifdef USE_SIMDE +-#include "lib/x86/sse2.h" ++#include + #else + #include + #endif diff --git a/biology/py-macs3/files/patch-pyproject.toml b/biology/py-macs3/files/patch-pyproject.toml new file mode 100644 index 000000000000..cf54cae8892f --- /dev/null +++ b/biology/py-macs3/files/patch-pyproject.toml @@ -0,0 +1,6 @@ +--- pyproject.toml.orig 2024-01-06 15:00:01 UTC ++++ pyproject.toml +@@ -1,2 +1,2 @@ + [build-system] +-requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython~=3.0', 'hmmlearn>=0.3'] ++requires=['setuptools>=60.0', 'numpy>=1.19', 'cykhash>=2.0,<3.0', 'Cython>=0', 'hmmlearn>=0.3'] diff --git a/biology/py-macs3/files/patch-requirements.txt b/biology/py-macs3/files/patch-requirements.txt new file mode 100644 index 000000000000..0c8106f79680 --- /dev/null +++ b/biology/py-macs3/files/patch-requirements.txt @@ -0,0 +1,8 @@ +--- requirements.txt.orig 2024-01-06 14:55:53 UTC ++++ requirements.txt +@@ -1,4 +1,4 @@ +-Cython~=3.0 ++Cython>=0 + numpy>=1.19 + hmmlearn>=0.3 + cykhash>=2.0,<3.0 diff --git a/biology/py-macs3/files/patch-setup.py b/biology/py-macs3/files/patch-setup.py new file mode 100644 index 000000000000..58dde13ba2c2 --- /dev/null +++ b/biology/py-macs3/files/patch-setup.py @@ -0,0 +1,20 @@ +--- setup.py.orig 2023-11-15 16:09:23 UTC ++++ setup.py +@@ -40,7 +40,7 @@ classifiers =[\ + install_requires = [ "numpy>=1.19", + "hmmlearn>=0.3", + "cykhash>=2.0,<3.0", +- "Cython~=3.0" ] ++ "Cython>=0" ] + + tests_requires = [ 'pytest' ] + +@@ -70,7 +70,7 @@ def main(): + + if not clang: + try: +- gcc_version_check = subprocess.check_output( ["gcc", "--version"], universal_newlines=True) ++ gcc_version_check = subprocess.check_output( ["cc", "--version"], universal_newlines=True) + if gcc_version_check.find("clang") != -1: + clang = True + else: diff --git a/biology/py-macs3/pkg-descr b/biology/py-macs3/pkg-descr new file mode 100644 index 000000000000..7e901a88e5ea --- /dev/null +++ b/biology/py-macs3/pkg-descr @@ -0,0 +1,6 @@ +MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying +transcription factor (TF) binding sites. Such sites are generated +by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq +(Assay for Transposase Accessible Chromatin Sequencing). MACS +identifies "peaks" in the genome sequence, which are areas enriched +in bound TFs or accessible chromatin.