diff --git a/biology/Makefile b/biology/Makefile index 802b08222e63..43554eb9416e 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,258 +1,257 @@ COMMENT = Biology SUBDIR += R-cran-Biobase SUBDIR += R-cran-BiocGenerics SUBDIR += R-cran-BiocManager SUBDIR += TrimGalore SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += andi 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 += chip-seq SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += coverm SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasda SUBDIR += fasda-utils SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastani SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastq-trim SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fermi-lite SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gffread SUBDIR += gkl 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 += mca-calling 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 += 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-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += preseq 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-newick SUBDIR += py-ont-fast5-api SUBDIR += py-pandas-charm SUBDIR += py-py2bit SUBDIR += py-pybigwig SUBDIR += py-pydeseq2 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 += 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 += seqkit SUBDIR += seqtk SUBDIR += seqwish SUBDIR += sigviewer SUBDIR += slclust SUBDIR += smithwaterman 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-macs2/Makefile b/biology/py-macs2/Makefile deleted file mode 100644 index a3795d4921ed..000000000000 --- a/biology/py-macs2/Makefile +++ /dev/null @@ -1,40 +0,0 @@ -PORTNAME= macs2 -DISTVERSIONPREFIX= v -DISTVERSION= 2.2.9.1 -PORTREVISION= 3 -CATEGORIES= biology python -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} - -MAINTAINER= jwb@FreeBSD.org -COMMENT= Identify transcription factor binding sites -WWW= https://github.com/taoliu/MACS - -LICENSE= BSD3CLAUSE -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Depends on expired lang/cython0 -EXPIRATION_DATE=2026-09-15 - -BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} -RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}cykhash>0:devel/py-cykhash@${PY_FLAVOR} -TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} \ - bash:shells/bash - -USES= python shebangfix -USE_GITHUB= yes -USE_PYTHON= autoplist concurrent cython0 distutils - -GH_ACCOUNT= taoliu -GH_PROJECT= MACS -SHEBANG_FILES= test/cmdlinetest_update test/cmdlinetest test/prockreport - -post-stage: - ${STRIP_CMD} \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*.so \ - ${STAGEDIR}${PYTHON_SITELIBDIR}/MACS2/*/*.so - -do-test: install - @cd ${WRKSRC}/test && ./cmdlinetest tag - -.include diff --git a/biology/py-macs2/distinfo b/biology/py-macs2/distinfo deleted file mode 100644 index e6da44033e73..000000000000 --- a/biology/py-macs2/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1691269587 -SHA256 (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 8e461dde82288280fe708cd4f5fec986fbf2da67b344f4dea5693af849549163 -SIZE (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 133109075 diff --git a/biology/py-macs2/pkg-descr b/biology/py-macs2/pkg-descr deleted file mode 100644 index 0310d2e092f8..000000000000 --- a/biology/py-macs2/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -MACS is a tool for chromatin immunoprecipitation (ChIP) sequence analysis. -MACS empirically models the length of the sequenced ChIP fragments, which -tend to be shorter than sonication or library construction size estimates, -and uses it to improve the spatial resolution of predicted binding sites.