From owner-svn-ports-all@freebsd.org Tue Jul 3 08:42:56 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 1C6D5102A7B3; Tue, 3 Jul 2018 08:42:56 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id B9F40745A8; Tue, 3 Jul 2018 08:42:55 +0000 (UTC) (envelope-from yuri@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 mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 94CBC19D49; Tue, 3 Jul 2018 08:42:55 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w638gttG020159; Tue, 3 Jul 2018 08:42:55 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w638gsNn020155; Tue, 3 Jul 2018 08:42:54 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201807030842.w638gsNn020155@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Tue, 3 Jul 2018 08:42:54 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r473806 - in head/biology: . cytoscape X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . cytoscape X-SVN-Commit-Revision: 473806 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 03 Jul 2018 08:42:56 -0000 Author: yuri Date: Tue Jul 3 08:42:54 2018 New Revision: 473806 URL: https://svnweb.freebsd.org/changeset/ports/473806 Log: New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression Added: head/biology/cytoscape/ head/biology/cytoscape/Makefile (contents, props changed) head/biology/cytoscape/distinfo (contents, props changed) head/biology/cytoscape/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Tue Jul 3 08:37:35 2018 (r473805) +++ head/biology/Makefile Tue Jul 3 08:42:54 2018 (r473806) @@ -22,6 +22,7 @@ SUBDIR += clustalw SUBDIR += clustalx SUBDIR += consed + SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += emboss Added: head/biology/cytoscape/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cytoscape/Makefile Tue Jul 3 08:42:54 2018 (r473806) @@ -0,0 +1,59 @@ +# $FreeBSD$ + +PORTNAME= cytoscape +DISTVERSION= 3.6.1 +CATEGORIES= biology java +MASTER_SITES= LOCAL/yuri/:maven \ + http://people.freebsd.org/~yuri/:maven +DISTFILES= FreeBSD-${PORTNAME}-${PORTVERSION}-maven-repository.tar.gz:maven + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Software to visualize molecular interaction networks, gene expression + +LICENSE= MIT +xLICENSE_FILE= ${WRKSRC}/license.txt + +BUILD_DEPENDS= mvn:devel/maven \ + bash:shells/bash +RUN_DEPENDS= bash:shells/bash + +USES= shebangfix +SHEBANG_FILES= gui-distribution/assembly/src/main/bin/cytoscape.sh +USE_JAVA= yes +JAVA_VERSION= 1.7+ +USE_GITHUB= yes +GH_TUPLE= ${PORTNAME}:${PORTNAME}-parent:${DISTVERSION}:p/parent \ + ${PORTNAME}:${PORTNAME}-api:${DISTVERSION}:a/api \ + ${PORTNAME}:${PORTNAME}-impl:${DISTVERSION}:i/impl \ + ${PORTNAME}:${PORTNAME}-support:${DISTVERSION}:s/support \ + ${PORTNAME}:${PORTNAME}-gui-distribution:${DISTVERSION}:g/gui-distribution \ + ${PORTNAME}:${PORTNAME}-app-template:${DISTVERSION}:d/app-developer +NO_ARCH= yes + +USER_WRKDIR= ~/.${PORTNAME} + +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \ + ${LOCALBASE}/bin/mvn --offline \ + -fae install \ + -Dmaven.test.skip=true \ + -Duser.home=${WRKDIR} + +do-install: + @cd ${WRKSRC} && ${COPYTREE_SHARE} gui-distribution ${STAGEDIR}${DATADIR} + # shouldn't be needed, but the executable bit sometimes isn't set + @${CHMOD} +x ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/cytoscape.sh + @${CHMOD} +x ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework/bin/karaf + # create a shell executable calling the real command + @(echo "#!/bin/sh"; \ + echo ""; \ + echo "cd ${DATADIR} && JAVA_HOME=${JAVA_HOME} ./gui-distribution/assembly/target/cytoscape/cytoscape.sh \"$@\"" \ + ) > ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + @${CHMOD} +x ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + # redirect user data to /tmp until they fix the location so that it would write under $HOME + @${RM} -r ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework/instances + @cd ${STAGEDIR}${DATADIR}/gui-distribution/assembly/target/cytoscape/framework && ${LN} -s /tmp instances + # use the automatic plist: a few hundred files are under DATADIR + @${SETENV} ${CO_ENV} ${SH} ${SCRIPTSDIR}/check-stagedir.sh makeplist | ${GREP} -v ^\/ | ${SED} -e 's|%%DATADIR%%|share/${PORTNAME}|' > ${TMPPLIST} + +.include Added: head/biology/cytoscape/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cytoscape/distinfo Tue Jul 3 08:42:54 2018 (r473806) @@ -0,0 +1,17 @@ +TIMESTAMP = 1530603760 +SHA256 (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = f3e33e99168b56768d2ee854956e59bcbb888101fd518239887524d692b78f7a +SIZE (FreeBSD-cytoscape-3.6.1-maven-repository.tar.gz) = 1235655281 +SHA256 (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = f172c9e459293661a83d2618da511901410336b76b0c1716697e60f821c2f150 +SIZE (cytoscape-cytoscape-3.6.1_GH0.tar.gz) = 12785 +SHA256 (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 0786e8d7877fa54d2a64d65209856a4a946df4facd3cbc947e8c65d14a035084 +SIZE (cytoscape-cytoscape-parent-3.6.1_GH0.tar.gz) = 2863 +SHA256 (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = a264a434d5942cad2ef69df7aa29fad74a6d1f11369a964d7c38462608def73b +SIZE (cytoscape-cytoscape-api-3.6.1_GH0.tar.gz) = 1731631 +SHA256 (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 0fcea5a4d804972db5b0cf77174a953d22da8fed6740dbaa01754eb7aea50d21 +SIZE (cytoscape-cytoscape-impl-3.6.1_GH0.tar.gz) = 29851040 +SHA256 (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 3f13088c35d41fa616dc7e735469f360ee4d17b1838cde8291f88b01bacfe657 +SIZE (cytoscape-cytoscape-support-3.6.1_GH0.tar.gz) = 52940 +SHA256 (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 73fb7efb51a0413252a7e9e28d4fb7e28d16eea9f60be534fd962a5e534ca72e +SIZE (cytoscape-cytoscape-gui-distribution-3.6.1_GH0.tar.gz) = 14818052 +SHA256 (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 9cf7b64a3e6effd22a20d577c7fa41b11f896e2298ef1655f2fe31c21602bce0 +SIZE (cytoscape-cytoscape-app-template-3.6.1_GH0.tar.gz) = 1887 Added: head/biology/cytoscape/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cytoscape/pkg-descr Tue Jul 3 08:42:54 2018 (r473806) @@ -0,0 +1,6 @@ +Cytoscape is an open source software platform for visualizing complex networks +and integrating these with any type of attribute data. A lot of Apps are +available for various kinds of problem domains, including bioinformatics, social +network analysis, and semantic web. + +WWW: http://www.cytoscape.org