From owner-svn-ports-head@freebsd.org Thu Mar 17 08:21:16 2016 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 2A79EAD489C; Thu, 17 Mar 2016 08:21:16 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 02444C98; Thu, 17 Mar 2016 08:21:15 +0000 (UTC) (envelope-from wen@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u2H8LF3r023341; Thu, 17 Mar 2016 08:21:15 GMT (envelope-from wen@FreeBSD.org) Received: (from wen@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u2H8LELo023336; Thu, 17 Mar 2016 08:21:14 GMT (envelope-from wen@FreeBSD.org) Message-Id: <201603170821.u2H8LELo023336@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: wen set sender to wen@FreeBSD.org using -f From: Wen Heping Date: Thu, 17 Mar 2016 08:21:14 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r411261 - in head/biology: . trimmomatic X-SVN-Group: ports-head 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: 2.1.21 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: Thu, 17 Mar 2016 08:21:16 -0000 Author: wen Date: Thu Mar 17 08:21:14 2016 New Revision: 411261 URL: https://svnweb.freebsd.org/changeset/ports/411261 Log: Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com Added: head/biology/trimmomatic/ head/biology/trimmomatic/Makefile (contents, props changed) head/biology/trimmomatic/distinfo (contents, props changed) head/biology/trimmomatic/pkg-descr (contents, props changed) head/biology/trimmomatic/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Mar 17 07:03:42 2016 (r411260) +++ head/biology/Makefile Thu Mar 17 08:21:14 2016 (r411261) @@ -95,6 +95,7 @@ SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += treeviewx + SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet Added: head/biology/trimmomatic/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/trimmomatic/Makefile Thu Mar 17 08:21:14 2016 (r411261) @@ -0,0 +1,27 @@ +# Created by: Dan Siercks +# $FreeBSD$ + +PORTNAME= trimmomatic +PORTVERSION= 0.35 +CATEGORIES= biology java +MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/ +DISTNAME= Trimmomatic-${PORTVERSION} + +MAINTAINER= bacon4000@gmail.com +COMMENT= Flexible read trimming tool for Illumina NGS data + +LICENSE= GPLv3 + +USES= zip +USE_JAVA= yes +JAVA_VERSION= 1.6+ +JAVA_RUN= yes +NO_BUILD= yes +NO_ARCH= yes + +do-install: + ${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \ + ${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar + cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR} + +.include Added: head/biology/trimmomatic/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/trimmomatic/distinfo Thu Mar 17 08:21:14 2016 (r411261) @@ -0,0 +1,2 @@ +SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69 +SIZE (Trimmomatic-0.35.zip) = 129810 Added: head/biology/trimmomatic/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/trimmomatic/pkg-descr Thu Mar 17 08:21:14 2016 (r411261) @@ -0,0 +1,4 @@ +Trimmomatic performs a variety of useful trimming tasks for illumina +NGS paired-end and single ended data. + +WWW: http://www.usadellab.org/cms/?page=trimmomatic Added: head/biology/trimmomatic/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/trimmomatic/pkg-plist Thu Mar 17 08:21:14 2016 (r411261) @@ -0,0 +1,7 @@ +%%DATADIR%%/adapters/NexteraPE-PE.fa +%%DATADIR%%/adapters/TruSeq2-PE.fa +%%DATADIR%%/adapters/TruSeq2-SE.fa +%%DATADIR%%/adapters/TruSeq3-PE-2.fa +%%DATADIR%%/adapters/TruSeq3-PE.fa +%%DATADIR%%/adapters/TruSeq3-SE.fa +%%JAVAJARDIR%%/trimmomatic.jar