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Sun, 4 Nov 2018 22:55:25 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id wA4MtObo024197; Sun, 4 Nov 2018 22:55:24 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201811042255.wA4MtObo024197@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 4 Nov 2018 22:55:24 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r484156 - in head/biology/igv: . files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology/igv: . files X-SVN-Commit-Revision: 484156 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 6D1FF8BB65 X-Spamd-Result: default: False [-0.59 / 200.00]; ARC_NA(0.00)[]; FROM_HAS_DN(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_MATCH_ENVRCPT_ALL(0.00)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_NONE(0.00)[]; HAS_XAW(0.00)[]; R_SPF_SOFTFAIL(0.00)[~all]; DMARC_NA(0.00)[FreeBSD.org]; RCVD_COUNT_THREE(0.00)[4]; MX_GOOD(-0.01)[cached: mx1.FreeBSD.org]; NEURAL_HAM_SHORT(-0.48)[-0.478,0]; FROM_EQ_ENVFROM(0.00)[]; R_DKIM_NA(0.00)[]; RCVD_TLS_LAST(0.00)[] X-Rspamd-Server: mx1.freebsd.org X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 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: Sun, 04 Nov 2018 22:55:26 -0000 Author: yuri Date: Sun Nov 4 22:55:24 2018 New Revision: 484156 URL: https://svnweb.freebsd.org/changeset/ports/484156 Log: biology/igv: Update 2.4.10 -> 2.4.15 Port changes: * Change to gradle, corresponding updates in build, install, environment, etc. Reported by: portscout Deleted: head/biology/igv/files/patch-build.xml Modified: head/biology/igv/Makefile head/biology/igv/distinfo Modified: head/biology/igv/Makefile ============================================================================== --- head/biology/igv/Makefile Sun Nov 4 22:53:52 2018 (r484155) +++ head/biology/igv/Makefile Sun Nov 4 22:55:24 2018 (r484156) @@ -2,9 +2,9 @@ PORTNAME= igv DISTVERSIONPREFIX= v -DISTVERSION= 2.4.10 +DISTVERSION= 2.4.15 CATEGORIES= biology java -MASTER_SITES= http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img +MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img DISTFILES= tools.png:img DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -15,32 +15,39 @@ COMMENT= Visualization tool for genomic datasets LICENSE= MIT LICENSE_FILE= ${WRKSRC}/license.txt -BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel +BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel \ + gradle:devel/gradle RUN_DEPENDS= openjfx8-devel>0:java/openjfx8-devel USES= gettext-runtime USE_GITHUB= yes GH_ACCOUNT= igvteam USE_JAVA= yes -USE_ANT= yes NO_ARCH= yes +MAKE_ENV+= GRADLE_USER_HOME=${WRKDIR} + SUB_FILES= ${PORTNAME}.sh DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \ "Biology;Science;" true PLIST_FILES= bin/${PORTNAME} \ - ${JAVAJARDIR}/batik-codec__V1.7.jar \ - ${JAVAJARDIR}/goby-io-igv__V1.0.jar \ + ${JAVAJARDIR}/batik-codec-1.10.jar \ + ${JAVAJARDIR}/goby-io-igv-1.1.jar \ + ${JAVAJARDIR}/log4j-core-2.11.0.jar \ ${JAVAJARDIR}/${PORTNAME}.jar \ share/pixmaps/igv.png +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle createDist + do-install: ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME} - ${INSTALL_DATA} ${WRKSRC}/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR} - ${INSTALL_DATA} ${WRKSRC}/batik-codec__V1.7.jar ${STAGEDIR}${JAVAJARDIR} - ${INSTALL_DATA} ${WRKSRC}/goby-io-igv__V1.0.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/batik-codec-1.10.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/goby-io-igv-1.1.jar ${STAGEDIR}${JAVAJARDIR} + ${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/log4j-core-2.11.0.jar ${STAGEDIR}${JAVAJARDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png .include Modified: head/biology/igv/distinfo ============================================================================== --- head/biology/igv/distinfo Sun Nov 4 22:53:52 2018 (r484155) +++ head/biology/igv/distinfo Sun Nov 4 22:55:24 2018 (r484156) @@ -1,5 +1,5 @@ -TIMESTAMP = 1529969906 -SHA256 (igv-2.4.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c -SIZE (igv-2.4.10/tools.png) = 5139 -SHA256 (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 2547050f768384ea14f88962476c6935115e6b2e35322874e4a93c6da7194e73 -SIZE (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 152822902 +TIMESTAMP = 1541357814 +SHA256 (igv-2.4.15/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.4.15/tools.png) = 5139 +SHA256 (igv-2.4.15/igvteam-igv-v2.4.15_GH0.tar.gz) = 8cd1da4a90b3607fd1d2840877497afa8a11b2bdbb69d1ead02ca401153ce6b0 +SIZE (igv-2.4.15/igvteam-igv-v2.4.15_GH0.tar.gz) = 141294377