Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 466448) +++ head/biology/Makefile (revision 466449) @@ -1,127 +1,128 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux SUBDIR += diamond SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += grappa SUBDIR += hmmer SUBDIR += htslib SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += molden SUBDIR += mopac SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-toolkit SUBDIR += njplot SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Coordinate 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-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml + SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += plinkseq SUBDIR += primer3 SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-macs2 SUBDIR += py-pysam SUBDIR += pycogent SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/pear-merger/Makefile =================================================================== --- head/biology/pear-merger/Makefile (nonexistent) +++ head/biology/pear-merger/Makefile (revision 466449) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +# Newer versions require registration to download and the site is unreliable. + +PORTNAME= pear +DISTVERSION= 0.9.6 +CATEGORIES= biology +MASTER_SITES= https://depot.galaxyproject.org/software/pear/ +PKGNAMESUFFIX= -merger +DISTNAME= ${PORTNAME}_${PORTVERSION}_src_all + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Memory-efficient and highly accurate paired-end read merger + +LICENSE= CC-BY-NC-SA-3.0 + +GNU_CONFIGURE= yes + +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}-src + +PLIST_FILES= bin/pearRM man/man1/pearRM.1.gz + +do-install: + @${CP} ${WRKSRC}/man/pear.1 ${WRKSRC}/man/pearRM.1 + ${INSTALL_PROGRAM} ${WRKSRC}/src/pear ${STAGEDIR}${PREFIX}/bin/pearRM + ${INSTALL_MAN} ${WRKSRC}/man/pearRM.1 ${STAGEDIR}${MANPREFIX}/man/man1 + +.include Property changes on: head/biology/pear-merger/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/pear-merger/distinfo =================================================================== --- head/biology/pear-merger/distinfo (nonexistent) +++ head/biology/pear-merger/distinfo (revision 466449) @@ -0,0 +1,3 @@ +TIMESTAMP = 1519766031 +SHA256 (pear_0.9.6_src_all.tar.gz) = f7728371e26a5b46fa928b0f7ae1b552ed6a78815b117ba48ef1af98e96c8e2b +SIZE (pear_0.9.6_src_all.tar.gz) = 292790 Property changes on: head/biology/pear-merger/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/pear-merger/pkg-descr =================================================================== --- head/biology/pear-merger/pkg-descr (nonexistent) +++ head/biology/pear-merger/pkg-descr (revision 466449) @@ -0,0 +1,5 @@ +PEAR is an ultrafast, memory-efficient and highly accurate paired-end read +merger. It is fully parallelized and can run with as low as just a few +kilobytes of memory. + +WWW: http://sco.h-its.org/exelixis/web/software/pear/ Property changes on: head/biology/pear-merger/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