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Bacon" Date: Sat, 9 Dec 2017 13:23:32 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r455857 - in head/biology: . p5-TrimGalore X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . p5-TrimGalore X-SVN-Commit-Revision: 455857 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 09 Dec 2017 13:23:34 -0000 Author: jwb Date: Sat Dec 9 13:23:32 2017 New Revision: 455857 URL: https://svnweb.freebsd.org/changeset/ports/455857 Log: [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming Approved by: jrm (mentor) Differential Revision: D13400 Added: head/biology/p5-TrimGalore/ head/biology/p5-TrimGalore/Makefile (contents, props changed) head/biology/p5-TrimGalore/distinfo (contents, props changed) head/biology/p5-TrimGalore/pkg-descr (contents, props changed) head/biology/p5-TrimGalore/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Dec 9 13:12:12 2017 (r455856) +++ head/biology/Makefile Sat Dec 9 13:23:32 2017 (r455857) @@ -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 Added: head/biology/p5-TrimGalore/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-TrimGalore/Makefile Sat Dec 9 13:23:32 2017 (r455857) @@ -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 Added: head/biology/p5-TrimGalore/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-TrimGalore/distinfo Sat Dec 9 13:23:32 2017 (r455857) @@ -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 Added: head/biology/p5-TrimGalore/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-TrimGalore/pkg-descr Sat Dec 9 13:23:32 2017 (r455857) @@ -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 Added: head/biology/p5-TrimGalore/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-TrimGalore/pkg-plist Sat Dec 9 13:23:32 2017 (r455857) @@ -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