Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 455856) +++ head/biology/Makefile (revision 455857) @@ -1,120 +1,121 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += ariadne SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += blat SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa 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 += 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 += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtools SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet SUBDIR += wise SUBDIR += xmolwt .include Index: head/biology/p5-TrimGalore/Makefile =================================================================== --- head/biology/p5-TrimGalore/Makefile (nonexistent) +++ head/biology/p5-TrimGalore/Makefile (revision 455857) @@ -0,0 +1,31 @@ +# $FreeBSD$ + +PORTNAME= TrimGalore +DISTVERSION= 0.4.5 +CATEGORIES= biology perl5 +PKGNAMEPREFIX= p5- + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Wrapper around Cutadapt and FastQC for adapter and quality trimming + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \ + fastqc>0:biology/fastqc + +NO_ARCH= yes +NO_BUILD= yes + +USES= perl5 python:env shebangfix +SHEBANG_FILES= trim_galore +USE_PERL5= run + +USE_GITHUB= yes +GH_ACCOUNT= FelixKrueger + +do-install: + ${INSTALL_SCRIPT} ${WRKSRC}/trim_galore ${STAGEDIR}${PREFIX}/bin + cd ${WRKSRC} && ${COPYTREE_SHARE} test_files ${STAGEDIR}${DATADIR} + +.include Property changes on: head/biology/p5-TrimGalore/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/p5-TrimGalore/distinfo =================================================================== --- head/biology/p5-TrimGalore/distinfo (nonexistent) +++ head/biology/p5-TrimGalore/distinfo (revision 455857) @@ -0,0 +1,3 @@ +TIMESTAMP = 1512570215 +SHA256 (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c +SIZE (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = 21983909 Property changes on: head/biology/p5-TrimGalore/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/p5-TrimGalore/pkg-descr =================================================================== --- head/biology/p5-TrimGalore/pkg-descr (nonexistent) +++ head/biology/p5-TrimGalore/pkg-descr (revision 455857) @@ -0,0 +1,4 @@ +Wrapper around Cutadapt and FastQC to consistently apply adapter and quality +trimming to FastQ files, with extra functionality for RRBS data. + +WWW: https://github.com/FelixKrueger/TrimGalore Property changes on: head/biology/p5-TrimGalore/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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/p5-TrimGalore/pkg-plist =================================================================== --- head/biology/p5-TrimGalore/pkg-plist (nonexistent) +++ head/biology/p5-TrimGalore/pkg-plist (revision 455857) @@ -0,0 +1,8 @@ +bin/trim_galore +%%DATADIR%%/test_files/4_seqs_with_Ns.fastq.gz +%%DATADIR%%/test_files/colorspace_file.fastq +%%DATADIR%%/test_files/empty_file.fastq +%%DATADIR%%/test_files/illumina_100K.fastq.gz +%%DATADIR%%/test_files/nextera_100K.fastq.gz +%%DATADIR%%/test_files/smallRNA_100K.fastq.gz +%%DATADIR%%/test_files/truncated.fq.gz Property changes on: head/biology/p5-TrimGalore/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +on \ 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