--- biology/igv/Makefile (revision 554705) +++ biology/igv/Makefile (working copy) @@ -2,7 +2,7 @@ PORTNAME= igv DISTVERSIONPREFIX= v -DISTVERSION= 2.5.3 +DISTVERSION= 2.8.10 CATEGORIES= biology java MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img DISTFILES= tools.png:img @@ -15,42 +15,31 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/license.txt -DEPRECATED= depends on expiring java/openjfx8-devel -EXPIRATION_DATE= 2020-11-30 +BUILD_DEPENDS= gradle>=6:devel/gradle -BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel \ - gradle4:devel/gradle4 -RUN_DEPENDS= openjfx8-devel>0:java/openjfx8-devel - USES= gettext-runtime USE_GITHUB= yes GH_ACCOUNT= igvteam -USE_JAVA= yes +USE_JAVA= 11 NO_ARCH= yes MAKE_ENV+= GRADLE_USER_HOME=${WRKDIR} SUB_FILES= ${PORTNAME}.sh +SUB_LIST= JAVA_HOME=${JAVA_HOME} \ + JAVAJARDIR=${JAVAJARDIR} DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \ "Biology;Science;" true -PLIST_FILES= bin/${PORTNAME} \ - ${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} gradle4 createDist + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} JAVA_VERSION=${JAVA_VERSION} gradle --no-daemon createDist do-install: + @${MKDIR} ${STAGEDIR}${JAVAJARDIR}/igv ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME} - ${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} + cd ${WRKSRC}/build/IGV-dist/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${JAVAJARDIR}/igv + ${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/igv.args ${STAGEDIR}${JAVAJARDIR}/igv ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png .include --- biology/igv/distinfo (revision 554705) +++ biology/igv/distinfo (working copy) @@ -1,5 +1,5 @@ -TIMESTAMP = 1559404148 -SHA256 (igv-2.5.3/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c -SIZE (igv-2.5.3/tools.png) = 5139 -SHA256 (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = fe7d19163e3abf798c8ea0606f0bc288aee40f86553c0b533b08b90d8b0b6c38 -SIZE (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = 140855739 +TIMESTAMP = 1604225095 +SHA256 (igv-2.8.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.8.10/tools.png) = 5139 +SHA256 (igv-2.8.10/igvteam-igv-v2.8.10_GH0.tar.gz) = 9a5654ae45be16bda17a5ed0df6c89c1b9f6a44371ca31393f1245dd47289c3d +SIZE (igv-2.8.10/igvteam-igv-v2.8.10_GH0.tar.gz) = 122360807 --- biology/igv/files/igv.sh.in (revision 554705) +++ biology/igv/files/igv.sh.in (working copy) @@ -1,9 +1,6 @@ #!/bin/sh -LANG=C -# phymem=$(free -m | awk '/^Mem:/{print $2}') -#igvmem=$(($phymem / 3)) -# ARGS=-Xmx${igvmem}m -java $ARGS \ - -Dapple.laf.useScreenMenuBar=true \ - -Djava.net.preferIPv4Stack=true \ - -jar %%JAVAJARDIR%%/igv.jar +%%JAVA_HOME%%/bin/java -showversion --module-path="%%JAVAJARDIR%%/igv" -Xmx4g \ + @"%%JAVAJARDIR%%/igv/igv.args" \ + -Dapple.laf.useScreenMenuBar=true \ + -Djava.net.preferIPv4Stack=true \ + --module=org.igv/org.broad.igv.ui.Main "$@" --- biology/igv/pkg-plist (nonexistent) +++ biology/igv/pkg-plist (working copy) @@ -0,0 +1,260 @@ +bin/igv +%%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.jar +%%JAVAJARDIR%%/igv/apache-client-2.8.5.jar +%%JAVAJARDIR%%/igv/auth-2.8.5.jar +%%JAVAJARDIR%%/igv/aws-core-2.8.5.jar +%%JAVAJARDIR%%/igv/aws-json-protocol-2.8.5.jar +%%JAVAJARDIR%%/igv/aws-query-protocol-2.8.5.jar +%%JAVAJARDIR%%/igv/aws-xml-protocol-2.8.5.jar +%%JAVAJARDIR%%/igv/batik-awt-util-1.11.jar +%%JAVAJARDIR%%/igv/batik-codec-1.11.jar +%%JAVAJARDIR%%/igv/batik-constants-1.11.jar +%%JAVAJARDIR%%/igv/batik-dom-1.11.jar +%%JAVAJARDIR%%/igv/batik-ext-1.11.jar +%%JAVAJARDIR%%/igv/batik-i18n-1.11.jar +%%JAVAJARDIR%%/igv/batik-svggen-1.11.jar +%%JAVAJARDIR%%/igv/batik-transcoder-1.11.jar +%%JAVAJARDIR%%/igv/batik-util-1.11.jar +%%JAVAJARDIR%%/igv/batik-xml-1.11.jar +%%JAVAJARDIR%%/igv/cognitoidentity-2.8.5.jar +%%JAVAJARDIR%%/igv/commons-codec-1.11.jar +%%JAVAJARDIR%%/igv/commons-collections-20040616.jar +%%JAVAJARDIR%%/igv/commons-compress-1.19.jar +%%JAVAJARDIR%%/igv/commons-configuration-1.10.jar +%%JAVAJARDIR%%/igv/commons-io-2.6.jar +%%JAVAJARDIR%%/igv/commons-jexl-2.1.1.jar +%%JAVAJARDIR%%/igv/commons-lang-2.6.jar +%%JAVAJARDIR%%/igv/commons-lang3-3.9.jar +%%JAVAJARDIR%%/igv/commons-logging-1.2.jar +%%JAVAJARDIR%%/igv/commons-math3-3.6.1.jar +%%JAVAJARDIR%%/igv/dsiutils-2.3.3.jar +%%JAVAJARDIR%%/igv/eventstream-1.0.1.jar +%%JAVAJARDIR%%/igv/fastutil-7.0.12.jar +%%JAVAJARDIR%%/igv/genomes/1kg_ref.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/1kg_v37.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/1kg_v37_alias.tab +%%JAVAJARDIR%%/igv/genomes/ABaumannii_ATCC_17978.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ABaumannii_AYE_uid61637.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/AGPv3.31.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/AgamP3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Aplysia.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/B73.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/CCAF000000000.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/CE_1.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/CSavignyi_v2.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/D.discoideum.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/EBV_Type2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Foxy4287.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/GCF_000233375.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/GSM552910.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/GSM552910_alias.tab +%%JAVAJARDIR%%/igv/genomes/Glamblia_2.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/HHV4_Type1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ITAG2.3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ITAG2.3_alias.tab +%%JAVAJARDIR%%/igv/genomes/M74568.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/MusPutFur1.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/MusaAcuminata.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/MusaBalbisianaPKWv1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_000913.2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_000913.2_alias.tab +%%JAVAJARDIR%%/igv/genomes/NC_000913.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_000964.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_001405.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_001422.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_001623.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_001722.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_001802.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_002655.2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_002755.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_002929.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_003112.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_003116.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_004917.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_008601.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_008767.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_009012.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_009012_alias.tab +%%JAVAJARDIR%%/igv/genomes/NC_012920.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/NC_016856.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/O_Sativa_r6.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/OryCun2.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Pf3D7_v9.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Pf3D7_v9.0_alias.tab +%%JAVAJARDIR%%/igv/genomes/PlasmoDB_24.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/PlasmoDB_7.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/PlasmoDB_8.2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Plasmodium_3D7_v2.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Plasmodium_3D7_v5.5.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Plasmodium_6.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/SL2.31.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/SL2.40.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/U00096.2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/U00096.2_alias.tab +%%JAVAJARDIR%%/igv/genomes/VcholeraeN16961.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/WS201.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/WS220.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/WS220_alias.tab +%%JAVAJARDIR%%/igv/genomes/WS245.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/Y55.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ZmB73_5a.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ZmB73_5a_alias.tab +%%JAVAJARDIR%%/igv/genomes/anidulans_4.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/anidulans_4.1_alias.tab +%%JAVAJARDIR%%/igv/genomes/b37.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/b37_alias.tab +%%JAVAJARDIR%%/igv/genomes/bosTau3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/bosTau3_alias.tab +%%JAVAJARDIR%%/igv/genomes/bosTau4.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/bosTau4_alias.tab +%%JAVAJARDIR%%/igv/genomes/bosTau6.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/bosTau6_alias.tab +%%JAVAJARDIR%%/igv/genomes/bosTau7.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/bosTau7_alias.tab +%%JAVAJARDIR%%/igv/genomes/bosTau8.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ca21.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/canFam2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/canFam3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/candida.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/cavPor3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ce10.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ce11.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ce4.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ce6.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/danRer10.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/danRer11.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/danRer6.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/danRer7.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/dm2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/dm3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/dm6.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/dmel_5.9.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/dmel_r5.22.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/dmel_r5.33.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/equCab2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/felCat5.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/galGal3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/galGal4.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/galGal5.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/gasAcu1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/gmax10.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/gmax8.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/hg16.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/hg17.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/hg18.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/hg19.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/hg19_alias.tab +%%JAVAJARDIR%%/igv/genomes/hg38.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/laevis_7.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/lmjr.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/lmjr_4.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/lmjr_4.0_alias.tab +%%JAVAJARDIR%%/igv/genomes/me49.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/mg8.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/mm10.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/mm7.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/mm8.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/mm9.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/monDom5.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/nc10.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/nc10_alias.tab +%%JAVAJARDIR%%/igv/genomes/ncrassa_v3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/osativa_6.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/osativa_6.1_alias.tab +%%JAVAJARDIR%%/igv/genomes/osativa_7.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/oviAri3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/panTro2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/panTro3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/panTro4.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ppatens_1.2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/pvivax.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/pvivax_alias.tab +%%JAVAJARDIR%%/igv/genomes/rheMac2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/rheMac3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/rheMac8.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/rn4.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/rn5.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/rn6.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/sacCer1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/sacCer2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/sacCer2_alias.tab +%%JAVAJARDIR%%/igv/genomes/sacCer3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/sacCer3_alias.tab +%%JAVAJARDIR%%/igv/genomes/sacCer62.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/sacCer62_alias.tab +%%JAVAJARDIR%%/igv/genomes/sclerotiorum.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/sk1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/spombe_1.55.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/spombe_709.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/spur_2.1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/spur_2.5.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/spur_3.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/susScr3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/susScrofa.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/taeGut1.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tair10.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tair10_alias.tab +%%JAVAJARDIR%%/igv/genomes/tair8.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tair9.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tb427_4.2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tb927.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tbgambi.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tbgambi_4.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tbgambi_4.0_alias.tab +%%JAVAJARDIR%%/igv/genomes/tbrucei927_4.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tbrucei927_4.0_alias.tab +%%JAVAJARDIR%%/igv/genomes/tbrucei927_5.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tcas_2.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/tcas_3.0.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/vvinifera.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/ws241.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/xenTro2.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/xenTro9.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/zebrafish.chrom.sizes +%%JAVAJARDIR%%/igv/goby-io-3.3.1.jar +%%JAVAJARDIR%%/igv/gson-2.8.5.jar +%%JAVAJARDIR%%/igv/guava-27.0.1-jre.jar +%%JAVAJARDIR%%/igv/htsjdk-2.23.0.jar +%%JAVAJARDIR%%/igv/http-client-spi-2.8.5.jar +%%JAVAJARDIR%%/igv/httpclient-4.5.9.jar +%%JAVAJARDIR%%/igv/httpcore-4.4.11.jar +%%JAVAJARDIR%%/igv/icb-utils-2.0.2.jar +%%JAVAJARDIR%%/igv/igv.args +%%JAVAJARDIR%%/igv/igv.jar +%%JAVAJARDIR%%/igv/j2objc-annotations-1.1.jar +%%JAVAJARDIR%%/igv/jackson-annotations-2.9.0.jar +%%JAVAJARDIR%%/igv/jackson-core-2.9.8.jar +%%JAVAJARDIR%%/igv/jackson-databind-2.9.8.jar +%%JAVAJARDIR%%/igv/jide-common-3.7.3.jar +%%JAVAJARDIR%%/igv/jsap-3.0.0.jar +%%JAVAJARDIR%%/igv/log4j-1.2-api-2.11.0.jar +%%JAVAJARDIR%%/igv/log4j-api-2.11.0.jar +%%JAVAJARDIR%%/igv/log4j-core-2.11.0.jar +%%JAVAJARDIR%%/igv/netty-buffer-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-codec-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-codec-http-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-common-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-handler-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-nio-client-2.8.5.jar +%%JAVAJARDIR%%/igv/netty-reactive-streams-2.0.3.jar +%%JAVAJARDIR%%/igv/netty-reactive-streams-http-2.0.3.jar +%%JAVAJARDIR%%/igv/netty-resolver-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-transport-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.39.Final-linux-x86_64.jar +%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.39.Final.jar +%%JAVAJARDIR%%/igv/ngs-java-2.9.0.jar +%%JAVAJARDIR%%/igv/profiles-2.8.5.jar +%%JAVAJARDIR%%/igv/protobuf-java-3.7.0-rc1.jar +%%JAVAJARDIR%%/igv/protocol-core-2.8.5.jar +%%JAVAJARDIR%%/igv/reactive-streams-1.0.2.jar +%%JAVAJARDIR%%/igv/regions-2.8.5.jar +%%JAVAJARDIR%%/igv/s3-2.8.5.jar +%%JAVAJARDIR%%/igv/sdk-core-2.8.5.jar +%%JAVAJARDIR%%/igv/slf4j-api-1.7.26.jar +%%JAVAJARDIR%%/igv/slf4j-simple-1.7.26.jar +%%JAVAJARDIR%%/igv/snappy-java-1.1.7.3.jar +%%JAVAJARDIR%%/igv/sts-2.8.5.jar +%%JAVAJARDIR%%/igv/swing-layout-1.0.3.jar +%%JAVAJARDIR%%/igv/utils-2.8.5.jar +%%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar +share/pixmaps/igv.png