Attachment 219925 Details for Bug 250980 – Unified diff to 2.8.12

[patch] Unified diff to 2.8.12

igv.patch (text/plain), 16.29 KB, created by Jason W. Bacon on 2020-11-24 14:07:04 UTC

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Creator: Jason W. Bacon

Created: 2020-11-24 14:07:04 UTC

Size: 16.29 KB

patch

obsolete

>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/igv/Makefile /usr/ports/wip/igv/Makefile
>--- /usr/ports/biology/igv/Makefile	2020-03-19 04:33:13.000000000 -0500
>+++ /usr/ports/wip/igv/Makefile	2020-11-24 07:44:18.852984000 -0600
>@@ -2,7 +2,7 @@
> 
> PORTNAME=	igv
> DISTVERSIONPREFIX=	v
>-DISTVERSION=	2.5.3
>+DISTVERSION=	2.8.12
> 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/${PORTNAME}.png
> 
> .include <bsd.port.mk>
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/igv/distinfo /usr/ports/wip/igv/distinfo
>--- /usr/ports/biology/igv/distinfo	2019-06-01 15:49:20.000000000 -0500
>+++ /usr/ports/wip/igv/distinfo	2020-11-24 07:29:49.729173000 -0600
>@@ -1,5 +1,5 @@
>-TIMESTAMP = 1559404148
>-SHA256 (igv-2.5.3/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
>-SIZE (igv-2.5.3/tools.png) = 5139
>-SHA256 (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = fe7d19163e3abf798c8ea0606f0bc288aee40f86553c0b533b08b90d8b0b6c38
>-SIZE (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = 140855739
>+TIMESTAMP = 1606224589
>+SHA256 (igv-2.8.12/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
>+SIZE (igv-2.8.12/tools.png) = 5139
>+SHA256 (igv-2.8.12/igvteam-igv-v2.8.12_GH0.tar.gz) = e4bce21034fe011da3dad7beed0cfe3ad554e7c38e6187135747cfc487083248
>+SIZE (igv-2.8.12/igvteam-igv-v2.8.12_GH0.tar.gz) = 122358621
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/igv/files/igv.sh.in /usr/ports/wip/igv/files/igv.sh.in
>--- /usr/ports/biology/igv/files/igv.sh.in	2018-06-25 18:56:00.000000000 -0500
>+++ /usr/ports/wip/igv/files/igv.sh.in	2020-11-24 07:22:52.498097000 -0600
>@@ -1,9 +1,6 @@
> #!/bin/sh
>-LANG=C
>-# phymem=$(free -m | awk '/^Mem:/{print $2}')
>-#igvmem=$(($phymem / 3))
>-# ARGS=-Xmx${igvmem}m
>-java $ARGS \
>-  -Dapple.laf.useScreenMenuBar=true \
>-  -Djava.net.preferIPv4Stack=true \
>-  -jar %%JAVAJARDIR%%/igv.jar
>+%%JAVA_HOME%%/bin/java -showversion --module-path="%%JAVAJARDIR%%/igv" -Xmx4g \
>+    @"%%JAVAJARDIR%%/igv/igv.args" \
>+    -Dapple.laf.useScreenMenuBar=true \
>+    -Djava.net.preferIPv4Stack=true \
>+    --module=org.igv/org.broad.igv.ui.Main "$@"
>diff -ruN --exclude=CVS --exclude=.svn /usr/ports/biology/igv/pkg-plist /usr/ports/wip/igv/pkg-plist
>--- /usr/ports/biology/igv/pkg-plist	1969-12-31 18:00:00.000000000 -0600
>+++ /usr/ports/wip/igv/pkg-plist	2020-11-24 07:42:00.661388000 -0600
>@@ -0,0 +1,262 @@
>+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
>+%%JAVAJARDIR%%/igv/htsjdk-2.23.0.jar
>+%%JAVAJARDIR%%/igv/http-client-spi-2.15.9.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-2.10.4.jar
>+%%JAVAJARDIR%%/igv/jackson-core-2.10.4.jar
>+%%JAVAJARDIR%%/igv/jackson-databind-2.10.4.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/metrics-spi-2.15.9.jar
>+%%JAVAJARDIR%%/igv/netty-buffer-4.1.46.Final.jar
>+%%JAVAJARDIR%%/igv/netty-codec-4.1.46.Final.jar
>+%%JAVAJARDIR%%/igv/netty-codec-http-4.1.46.Final.jar
>+%%JAVAJARDIR%%/igv/netty-common-4.1.46.Final.jar
>+%%JAVAJARDIR%%/igv/netty-handler-4.1.46.Final.jar
>+%%JAVAJARDIR%%/igv/netty-nio-client-2.15.9.jar
>+%%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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Attachments on bug 250980: 219489 | 219925