Date: Mon, 30 Nov 2020 01:06:38 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r556609 - in head/biology/igv: . files Message-ID: <202011300106.0AU16cgm084986@repo.freebsd.org>
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Author: yuri Date: Mon Nov 30 01:06:37 2020 New Revision: 556609 URL: https://svnweb.freebsd.org/changeset/ports/556609 Log: biology/igv: 2.5.3 -> 2.8.13 PR: 250980 Added: head/biology/igv/pkg-plist (contents, props changed) Modified: head/biology/igv/Makefile head/biology/igv/distinfo head/biology/igv/files/igv.sh.in Modified: head/biology/igv/Makefile ============================================================================== --- head/biology/igv/Makefile Mon Nov 30 00:28:17 2020 (r556608) +++ head/biology/igv/Makefile Mon Nov 30 01:06:37 2020 (r556609) @@ -2,7 +2,7 @@ PORTNAME= igv DISTVERSIONPREFIX= v -DISTVERSION= 2.5.3 +DISTVERSION= 2.8.13 CATEGORIES= biology java MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img DISTFILES= tools.png:img @@ -15,17 +15,18 @@ COMMENT= Visualization tool for genomic datasets LICENSE= MIT LICENSE_FILE= ${WRKSRC}/license.txt -DEPRECATED= depends on expiring java/openjfx8-devel -EXPIRATION_DATE= 2020-11-30 +BUILD_DEPENDS= openjfx14>0:java/openjfx14 \ + gradle:devel/gradle +RUN_DEPENDS= openjfx14>0:java/openjfx14 -BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel \ - gradle4:devel/gradle4 -RUN_DEPENDS= openjfx8-devel>0:java/openjfx8-devel - USES= gettext-runtime +USE_JAVA= yes + USE_GITHUB= yes GH_ACCOUNT= igvteam -USE_JAVA= yes + +JAVA_VERSION= 11 + NO_ARCH= yes MAKE_ENV+= GRADLE_USER_HOME=${WRKDIR} @@ -35,22 +36,41 @@ 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-1.10.jar \ - ${JAVAJARDIR}/goby-io-igv-1.1.jar \ - ${JAVAJARDIR}/log4j-core-2.11.0.jar \ - ${JAVAJARDIR}/${PORTNAME}.jar \ - share/pixmaps/igv.png +# to rebuild the deps archive: +# 1. set DEV_UPDATE_MODE=yes +# 2. make makesum build +# 3. upload the *-deps archive +# 4. set DEV_UPDATE_MODE=no +# 5. make clean makesum +DEV_UPDATE_MODE= no + +DEPS_CACHE_DIR= ${WRKDIR} + +MAKE_ENV+= JAVA_HOME=${JAVA_HOME} +SUB_LIST= JAVA_HOME=${JAVA_HOME} + +.if (${DEV_UPDATE_MODE} == "yes") +post-build: + @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} + @${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" +.else +MASTER_SITES= LOCAL/yuri/:deps +DISTFILES+= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps +GRADLE_ARGS= --offline + +post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven + @cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} +.endif + do-build: - @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle4 createDist + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ + --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ + ${GRADLE_ARGS} --build-cache --stacktrace createDist do-install: ${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}/${PORTNAME} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png .include <bsd.port.mk> Modified: head/biology/igv/distinfo ============================================================================== --- head/biology/igv/distinfo Mon Nov 30 00:28:17 2020 (r556608) +++ head/biology/igv/distinfo Mon Nov 30 01:06:37 2020 (r556609) @@ -1,5 +1,7 @@ -TIMESTAMP = 1559404148 -SHA256 (igv-2.5.3/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c -SIZE (igv-2.5.3/tools.png) = 5139 -SHA256 (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = fe7d19163e3abf798c8ea0606f0bc288aee40f86553c0b533b08b90d8b0b6c38 -SIZE (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = 140855739 +TIMESTAMP = 1606697368 +SHA256 (igv-2.8.13/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.8.13/tools.png) = 5139 +SHA256 (igv-2.8.13/igv-2.8.13-deps.tar.gz) = 0bea74c4e1934fba8273c91ed9a6c2e88540b96823a8b8d4cf5c3d82617f330a +SIZE (igv-2.8.13/igv-2.8.13-deps.tar.gz) = 54089812 +SHA256 (igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz) = 891d3874ab2bc75d54c8f3ae8bc1df6b0b4b8b3f371d8699b17c69cbace77e7c +SIZE (igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz) = 122357224 Modified: head/biology/igv/files/igv.sh.in ============================================================================== --- head/biology/igv/files/igv.sh.in Mon Nov 30 00:28:17 2020 (r556608) +++ head/biology/igv/files/igv.sh.in Mon Nov 30 01:06:37 2020 (r556609) @@ -3,7 +3,8 @@ LANG=C # phymem=$(free -m | awk '/^Mem:/{print $2}') #igvmem=$(($phymem / 3)) # ARGS=-Xmx${igvmem}m -java $ARGS \ +%%JAVA_HOME%%/bin/java $ARGS \ + --module-path="%%JAVAJARDIR%%/igv" \ -Dapple.laf.useScreenMenuBar=true \ -Djava.net.preferIPv4Stack=true \ - -jar %%JAVAJARDIR%%/igv.jar + --module=org.igv/org.broad.igv.ui.Main Added: head/biology/igv/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/igv/pkg-plist Mon Nov 30 01:06:37 2020 (r556609) @@ -0,0 +1,261 @@ +bin/igv +%%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.jar +%%JAVAJARDIR%%/igv/apache-client-2.15.9.jar +%%JAVAJARDIR%%/igv/arns-2.15.9.jar +%%JAVAJARDIR%%/igv/auth-2.15.9.jar +%%JAVAJARDIR%%/igv/aws-core-2.15.9.jar +%%JAVAJARDIR%%/igv/aws-json-protocol-2.15.9.jar +%%JAVAJARDIR%%/igv/aws-query-protocol-2.15.9.jar +%%JAVAJARDIR%%/igv/aws-xml-protocol-2.15.9.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-2.15.9.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 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+%%JAVAJARDIR%%/igv/netty-reactive-streams-2.0.4.jar +%%JAVAJARDIR%%/igv/netty-reactive-streams-http-2.0.4.jar +%%JAVAJARDIR%%/igv/netty-resolver-4.1.46.Final.jar +%%JAVAJARDIR%%/igv/netty-transport-4.1.46.Final.jar +%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.46.Final-linux-x86_64.jar +%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.46.Final.jar +%%JAVAJARDIR%%/igv/ngs-java-2.9.0.jar +%%JAVAJARDIR%%/igv/profiles-2.15.9.jar +%%JAVAJARDIR%%/igv/protobuf-java-3.7.0-rc1.jar +%%JAVAJARDIR%%/igv/protocol-core-2.15.9.jar +%%JAVAJARDIR%%/igv/reactive-streams-1.0.3.jar +%%JAVAJARDIR%%/igv/regions-2.15.9.jar +%%JAVAJARDIR%%/igv/s3-2.15.9.jar +%%JAVAJARDIR%%/igv/sdk-core-2.15.9.jar +%%JAVAJARDIR%%/igv/slf4j-api-1.7.28.jar +%%JAVAJARDIR%%/igv/slf4j-simple-1.7.26.jar +%%JAVAJARDIR%%/igv/snappy-java-1.1.7.3.jar +%%JAVAJARDIR%%/igv/sts-2.15.9.jar +%%JAVAJARDIR%%/igv/swing-layout-1.0.3.jar +%%JAVAJARDIR%%/igv/utils-2.15.9.jar +%%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar +share/pixmaps/igv.png
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