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Bacon" Date: Sat, 14 Sep 2019 14:45:49 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r512018 - in head/biology/trimmomatic: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/trimmomatic: . files X-SVN-Commit-Revision: 512018 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: 2.1.29 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, 14 Sep 2019 14:45:50 -0000 Author: jwb Date: Sat Sep 14 14:45:49 2019 New Revision: 512018 URL: https://svnweb.freebsd.org/changeset/ports/512018 Log: biology/trimmomatic: Upgrade to 0.39 Add convenience script to run without knowing the location of the Java jar Added: head/biology/trimmomatic/files/ head/biology/trimmomatic/files/trimmomatic.in (contents, props changed) Modified: head/biology/trimmomatic/Makefile head/biology/trimmomatic/distinfo head/biology/trimmomatic/pkg-plist Modified: head/biology/trimmomatic/Makefile ============================================================================== --- head/biology/trimmomatic/Makefile Sat Sep 14 14:26:31 2019 (r512017) +++ head/biology/trimmomatic/Makefile Sat Sep 14 14:45:49 2019 (r512018) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= trimmomatic -PORTVERSION= 0.35 +DISTVERSION= 0.39 CATEGORIES= biology java MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/ DISTNAME= Trimmomatic-${PORTVERSION} @@ -11,17 +11,22 @@ MAINTAINER= jwb@FreeBSD.org COMMENT= Flexible read trimming tool for Illumina NGS data LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE USES= zip USE_JAVA= yes + JAVA_VERSION= 1.6+ JAVA_RUN= yes NO_BUILD= yes NO_ARCH= yes +SUB_FILES= trimmomatic + do-install: ${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \ ${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR} + ${INSTALL_SCRIPT} ${WRKDIR}/trimmomatic ${STAGEDIR}${PREFIX}/bin .include Modified: head/biology/trimmomatic/distinfo ============================================================================== --- head/biology/trimmomatic/distinfo Sat Sep 14 14:26:31 2019 (r512017) +++ head/biology/trimmomatic/distinfo Sat Sep 14 14:45:49 2019 (r512018) @@ -1,2 +1,3 @@ -SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69 -SIZE (Trimmomatic-0.35.zip) = 129810 +TIMESTAMP = 1568469691 +SHA256 (Trimmomatic-0.39.zip) = 2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca +SIZE (Trimmomatic-0.39.zip) = 133596 Added: head/biology/trimmomatic/files/trimmomatic.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/trimmomatic/files/trimmomatic.in Sat Sep 14 14:45:49 2019 (r512018) @@ -0,0 +1,3 @@ +#!/bin/sh -e + +java -jar %%PREFIX%%/share/java/classes/trimmomatic.jar "$@" Modified: head/biology/trimmomatic/pkg-plist ============================================================================== --- head/biology/trimmomatic/pkg-plist Sat Sep 14 14:26:31 2019 (r512017) +++ head/biology/trimmomatic/pkg-plist Sat Sep 14 14:45:49 2019 (r512018) @@ -1,7 +1,8 @@ +bin/trimmomatic +%%JAVAJARDIR%%/trimmomatic.jar %%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