diff --git a/biology/Makefile b/biology/Makefile index 4025c269aef3..4acd54fab965 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,200 +1,201 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += bioparser SUBDIR += biosoup SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps 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 += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac 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-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa 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 += wise .include diff --git a/biology/peak-classifier/Makefile b/biology/peak-classifier/Makefile new file mode 100644 index 000000000000..e964f1b7b49a --- /dev/null +++ b/biology/peak-classifier/Makefile @@ -0,0 +1,24 @@ +PORTNAME= peak-classifier +DISTVERSION= 0.1.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Classify ChIP/ATAC-Seq peaks based on features provided in a GFF + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libxtend.so:devel/libxtend libbiolibc.so:biology/biolibc +RUN_DEPENDS= bedtools:biology/bedtools \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} + +USES= localbase python:3.7+ shebangfix +USE_GITHUB= yes + +GH_ACCOUNT= auerlab +SHEBANG_FILES= feature-view.py + +pre-build: + cd ${WRKSRC} && make depend LOCALBASE=${LOCALBASE} + +.include diff --git a/biology/peak-classifier/distinfo b/biology/peak-classifier/distinfo new file mode 100644 index 000000000000..43f3d37e76fb --- /dev/null +++ b/biology/peak-classifier/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1623687381 +SHA256 (auerlab-peak-classifier-0.1.1_GH0.tar.gz) = 45230d50f204ecf1fa0f8bb1c96f00c25d84ae592b8def1cf053a07de60a8c7b +SIZE (auerlab-peak-classifier-0.1.1_GH0.tar.gz) = 86012 diff --git a/biology/peak-classifier/pkg-descr b/biology/peak-classifier/pkg-descr new file mode 100644 index 000000000000..b123dcbc554d --- /dev/null +++ b/biology/peak-classifier/pkg-descr @@ -0,0 +1,8 @@ +Classify ChIP/ATAC-Seq peaks based on features provided in a GFF + +Peaks are provided in a BED file sorted by chromosome and position. The GFF +must be sorted by chromosome and position, with gene-level features separated +by ### tags and each gene organized into subfeatures such as transcripts and +exons. This is the default for common data sources. + +WWW: https://github.com/auerlab/peak-classifier diff --git a/biology/peak-classifier/pkg-plist b/biology/peak-classifier/pkg-plist new file mode 100644 index 000000000000..787333471195 --- /dev/null +++ b/biology/peak-classifier/pkg-plist @@ -0,0 +1,9 @@ +bin/extract-genes +bin/feature-view +bin/filter-overlaps +bin/peak-classifier +libexec/extract-genes.awk +man/man1/extract-genes.1.gz +man/man1/feature-view.1.gz +man/man1/filter-overlaps.1.gz +man/man1/peak-classifier.1.gz