Index: head/biology/Makefile =================================================================== --- head/biology/Makefile +++ head/biology/Makefile @@ -73,6 +73,7 @@ SUBDIR += p5-Bio-SCF SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run + SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += phrap Index: head/biology/p5-TrimGalore/Makefile =================================================================== --- head/biology/p5-TrimGalore/Makefile +++ head/biology/p5-TrimGalore/Makefile @@ -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 Index: head/biology/p5-TrimGalore/distinfo =================================================================== --- head/biology/p5-TrimGalore/distinfo +++ head/biology/p5-TrimGalore/distinfo @@ -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 Index: head/biology/p5-TrimGalore/pkg-descr =================================================================== --- head/biology/p5-TrimGalore/pkg-descr +++ head/biology/p5-TrimGalore/pkg-descr @@ -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 Index: head/biology/p5-TrimGalore/pkg-plist =================================================================== --- head/biology/p5-TrimGalore/pkg-plist +++ head/biology/p5-TrimGalore/pkg-plist @@ -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