Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 568921) +++ head/biology/Makefile (revision 568922) @@ -1,190 +1,191 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools 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 += grappa 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 += lagan 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-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-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip 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-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python 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-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler 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 += seqio SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += spoa SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene + SUBDIR += vcf-split SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include Index: head/biology/vcf-split/Makefile =================================================================== --- head/biology/vcf-split/Makefile (nonexistent) +++ head/biology/vcf-split/Makefile (revision 568922) @@ -0,0 +1,23 @@ +# $FreeBSD$ + +PORTNAME= vcf-split +DISTVERSION= 0.1.1 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Split a multi-sample VCF into single-sample VCFs + +LICENSE= BSD2CLAUSE +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= biolibc>=0.1.1:biology/biolibc + +USE_GITHUB= yes +GH_ACCOUNT= auerlab + +PLIST_FILES= bin/vcf-split man/man1/vcf-split.1.gz + +pre-build: + (cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend) + +.include Property changes on: head/biology/vcf-split/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/vcf-split/distinfo =================================================================== --- head/biology/vcf-split/distinfo (nonexistent) +++ head/biology/vcf-split/distinfo (revision 568922) @@ -0,0 +1,3 @@ +TIMESTAMP = 1616331493 +SHA256 (auerlab-vcf-split-0.1.1_GH0.tar.gz) = 07fb3aff5bf6038b251baa6c0cbff0600487766838b497468ab06d300488f310 +SIZE (auerlab-vcf-split-0.1.1_GH0.tar.gz) = 14226 Property changes on: head/biology/vcf-split/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/vcf-split/pkg-descr =================================================================== --- head/biology/vcf-split/pkg-descr (nonexistent) +++ head/biology/vcf-split/pkg-descr (revision 568922) @@ -0,0 +1,8 @@ +Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands +of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF +with bcftools takes two days, so extracting the 137,977 samples one at a time +or using thousands of parallel readers of the same file is impractical. +Vcf-split solves this by generating thousands of single-sample outputs during +a single sweep through the multi-sample input. + +WWW: https://github.com/auerlab/vcf-split Property changes on: head/biology/vcf-split/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property