svn commit: r484156 - in head/biology/igv: . files
Yuri Victorovich
yuri at FreeBSD.org
Sun Nov 4 22:55:26 UTC 2018
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 <bsd.port.mk>
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
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