Attachment #219489 for bug #250980





PORTNAME=	igv
DISTVERSIONPREFIX=	v
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

LICENSE=	MIT
LICENSE_FILE=	${WRKSRC}/license.txt

BUILD_DEPENDS=	gradle>=6:devel/gradle
EXPIRATION_DATE=	2020-11-30

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=	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} ${MAKE_ENV} JAVA_VERSION=${JAVA_VERSION} gradle --no-daemon createDist

do-install:
	@${MKDIR} ${STAGEDIR}${JAVAJARDIR}/igv
	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
	cd ${WRKSRC}/build/IGV-dist/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${JAVAJARDIR}/igv
	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/igv.args ${STAGEDIR}${JAVAJARDIR}/igv
	${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>

Lines 1-5 Link Here

(-)biology/igv/distinfo (-5 / +5 lines)
1	TIMESTAMP = 1559404148	1	TIMESTAMP = 1604225095
2	SHA256 (igv-2.5.3/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c	2	SHA256 (igv-2.8.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
3	SIZE (igv-2.5.3/tools.png) = 5139	3	SIZE (igv-2.8.10/tools.png) = 5139
4	SHA256 (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = fe7d19163e3abf798c8ea0606f0bc288aee40f86553c0b533b08b90d8b0b6c38	4	SHA256 (igv-2.8.10/igvteam-igv-v2.8.10_GH0.tar.gz) = 9a5654ae45be16bda17a5ed0df6c89c1b9f6a44371ca31393f1245dd47289c3d
5	SIZE (igv-2.5.3/igvteam-igv-v2.5.3_GH0.tar.gz) = 140855739	5	SIZE (igv-2.8.10/igvteam-igv-v2.8.10_GH0.tar.gz) = 122360807

Lines 1-9 Link Here

(-)biology/igv/files/igv.sh.in (-8 / +5 lines)
1	#!/bin/sh	1	#!/bin/sh
2	LANG=C	2	%%JAVA_HOME%%/bin/java -showversion --module-path="%%JAVAJARDIR%%/igv" -Xmx4g \
3	# phymem=$(free -m \| awk '/^Mem:/{print $2}')	3	@"%%JAVAJARDIR%%/igv/igv.args" \
4	#igvmem=$(($phymem / 3))	4	-Dapple.laf.useScreenMenuBar=true \
5	# ARGS=-Xmx${igvmem}m	5	-Djava.net.preferIPv4Stack=true \
6	java $ARGS \	6	--module=org.igv/org.broad.igv.ui.Main "$@"
7	-Dapple.laf.useScreenMenuBar=true \
8	-Djava.net.preferIPv4Stack=true \
9	-jar %%JAVAJARDIR%%/igv.jar




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

Return to bug 250980

Lines 2-8 Link Here

(-)biology/igv/Makefile (-20 / +9 lines)
2		2
3	PORTNAME= igv	3	PORTNAME= igv
4	DISTVERSIONPREFIX= v	4	DISTVERSIONPREFIX= v
5	DISTVERSION= 2.5.3	5	DISTVERSION= 2.8.10
6	CATEGORIES= biology java	6	CATEGORIES= biology java
7	MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img	7	MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
8	DISTFILES= tools.png:img	8	DISTFILES= tools.png:img
Lines 15-56 Link Here
15	LICENSE= MIT	15	LICENSE= MIT
16	LICENSE_FILE= ${WRKSRC}/license.txt	16	LICENSE_FILE= ${WRKSRC}/license.txt
17		17
18	DEPRECATED= depends on expiring java/openjfx8-devel	18	BUILD_DEPENDS= gradle>=6:devel/gradle
19	EXPIRATION_DATE= 2020-11-30
20		19
21	BUILD_DEPENDS= openjfx8-devel>0:java/openjfx8-devel \
22	gradle4:devel/gradle4
23	RUN_DEPENDS= openjfx8-devel>0:java/openjfx8-devel
24
25	USES= gettext-runtime	20	USES= gettext-runtime
26	USE_GITHUB= yes	21	USE_GITHUB= yes
27	GH_ACCOUNT= igvteam	22	GH_ACCOUNT= igvteam
28	USE_JAVA= yes	23	USE_JAVA= 11
29	NO_ARCH= yes	24	NO_ARCH= yes
30		25
31	MAKE_ENV+= GRADLE_USER_HOME=${WRKDIR}	26	MAKE_ENV+= GRADLE_USER_HOME=${WRKDIR}
32		27
33	SUB_FILES= ${PORTNAME}.sh	28	SUB_FILES= ${PORTNAME}.sh
		29	SUB_LIST= JAVA_HOME=${JAVA_HOME} \
		30	JAVAJARDIR=${JAVAJARDIR}
34		31
35	DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \	32	DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \
36	"Biology;Science;" true	33	"Biology;Science;" true
37		34
38	PLIST_FILES= bin/${PORTNAME} \
39	${JAVAJARDIR}/batik-codec-1.10.jar \
40	${JAVAJARDIR}/goby-io-igv-1.1.jar \
41	${JAVAJARDIR}/log4j-core-2.11.0.jar \
42	${JAVAJARDIR}/${PORTNAME}.jar \
43	share/pixmaps/igv.png
44
45	do-build:	35	do-build:
46	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle4 createDist	36	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} JAVA_VERSION=${JAVA_VERSION} gradle --no-daemon createDist
47		37
48	do-install:	38	do-install:
		39	@${MKDIR} ${STAGEDIR}${JAVAJARDIR}/igv
49	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}	40	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
50	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR}	41	cd ${WRKSRC}/build/IGV-dist/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${JAVAJARDIR}/igv
51	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/batik-codec-1.10.jar ${STAGEDIR}${JAVAJARDIR}	42	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/igv.args ${STAGEDIR}${JAVAJARDIR}/igv
52	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/goby-io-igv-1.1.jar ${STAGEDIR}${JAVAJARDIR}
53	${INSTALL_DATA} ${WRKSRC}/build/IGV-dist/lib/log4j-core-2.11.0.jar ${STAGEDIR}${JAVAJARDIR}
54	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png	43	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png
55		44
56	.include <bsd.port.mk>	45	.include <bsd.port.mk>

Line 0 Link Here

(-)biology/igv/pkg-plist (+260 lines)
		1	bin/igv
		2	%%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.jar
		3	%%JAVAJARDIR%%/igv/apache-client-2.8.5.jar
		4	%%JAVAJARDIR%%/igv/auth-2.8.5.jar
		5	%%JAVAJARDIR%%/igv/aws-core-2.8.5.jar
		6	%%JAVAJARDIR%%/igv/aws-json-protocol-2.8.5.jar
		7	%%JAVAJARDIR%%/igv/aws-query-protocol-2.8.5.jar
		8	%%JAVAJARDIR%%/igv/aws-xml-protocol-2.8.5.jar
		9	%%JAVAJARDIR%%/igv/batik-awt-util-1.11.jar
		10	%%JAVAJARDIR%%/igv/batik-codec-1.11.jar
		11	%%JAVAJARDIR%%/igv/batik-constants-1.11.jar
		12	%%JAVAJARDIR%%/igv/batik-dom-1.11.jar
		13	%%JAVAJARDIR%%/igv/batik-ext-1.11.jar
		14	%%JAVAJARDIR%%/igv/batik-i18n-1.11.jar
		15	%%JAVAJARDIR%%/igv/batik-svggen-1.11.jar
		16	%%JAVAJARDIR%%/igv/batik-transcoder-1.11.jar
		17	%%JAVAJARDIR%%/igv/batik-util-1.11.jar
		18	%%JAVAJARDIR%%/igv/batik-xml-1.11.jar
		19	%%JAVAJARDIR%%/igv/cognitoidentity-2.8.5.jar
		20	%%JAVAJARDIR%%/igv/commons-codec-1.11.jar
		21	%%JAVAJARDIR%%/igv/commons-collections-20040616.jar
		22	%%JAVAJARDIR%%/igv/commons-compress-1.19.jar
		23	%%JAVAJARDIR%%/igv/commons-configuration-1.10.jar
		24	%%JAVAJARDIR%%/igv/commons-io-2.6.jar
		25	%%JAVAJARDIR%%/igv/commons-jexl-2.1.1.jar
		26	%%JAVAJARDIR%%/igv/commons-lang-2.6.jar
		27	%%JAVAJARDIR%%/igv/commons-lang3-3.9.jar
		28	%%JAVAJARDIR%%/igv/commons-logging-1.2.jar
		29	%%JAVAJARDIR%%/igv/commons-math3-3.6.1.jar
		30	%%JAVAJARDIR%%/igv/dsiutils-2.3.3.jar
		31	%%JAVAJARDIR%%/igv/eventstream-1.0.1.jar
		32	%%JAVAJARDIR%%/igv/fastutil-7.0.12.jar
		33	%%JAVAJARDIR%%/igv/genomes/1kg_ref.chrom.sizes
		34	%%JAVAJARDIR%%/igv/genomes/1kg_v37.chrom.sizes
		35	%%JAVAJARDIR%%/igv/genomes/1kg_v37_alias.tab
		36	%%JAVAJARDIR%%/igv/genomes/ABaumannii_ATCC_17978.chrom.sizes
		37	%%JAVAJARDIR%%/igv/genomes/ABaumannii_AYE_uid61637.chrom.sizes
		38	%%JAVAJARDIR%%/igv/genomes/AGPv3.31.chrom.sizes
		39	%%JAVAJARDIR%%/igv/genomes/AgamP3.chrom.sizes
		40	%%JAVAJARDIR%%/igv/genomes/Aplysia.chrom.sizes
		41	%%JAVAJARDIR%%/igv/genomes/B73.chrom.sizes
		42	%%JAVAJARDIR%%/igv/genomes/CCAF000000000.chrom.sizes
		43	%%JAVAJARDIR%%/igv/genomes/CE_1.0.chrom.sizes
		44	%%JAVAJARDIR%%/igv/genomes/CSavignyi_v2.1.chrom.sizes
		45	%%JAVAJARDIR%%/igv/genomes/D.discoideum.chrom.sizes
		46	%%JAVAJARDIR%%/igv/genomes/EBV_Type2.chrom.sizes
		47	%%JAVAJARDIR%%/igv/genomes/Foxy4287.chrom.sizes
		48	%%JAVAJARDIR%%/igv/genomes/GCF_000233375.1.chrom.sizes
		49	%%JAVAJARDIR%%/igv/genomes/GSM552910.chrom.sizes
		50	%%JAVAJARDIR%%/igv/genomes/GSM552910_alias.tab
		51	%%JAVAJARDIR%%/igv/genomes/Glamblia_2.0.chrom.sizes
		52	%%JAVAJARDIR%%/igv/genomes/HHV4_Type1.chrom.sizes
		53	%%JAVAJARDIR%%/igv/genomes/ITAG2.3.chrom.sizes
		54	%%JAVAJARDIR%%/igv/genomes/ITAG2.3_alias.tab
		55	%%JAVAJARDIR%%/igv/genomes/M74568.chrom.sizes
		56	%%JAVAJARDIR%%/igv/genomes/MusPutFur1.0.chrom.sizes
		57	%%JAVAJARDIR%%/igv/genomes/MusaAcuminata.chrom.sizes
		58	%%JAVAJARDIR%%/igv/genomes/MusaBalbisianaPKWv1.chrom.sizes
		59	%%JAVAJARDIR%%/igv/genomes/NC_000913.2.chrom.sizes
		60	%%JAVAJARDIR%%/igv/genomes/NC_000913.2_alias.tab
		61	%%JAVAJARDIR%%/igv/genomes/NC_000913.chrom.sizes
		62	%%JAVAJARDIR%%/igv/genomes/NC_000964.chrom.sizes
		63	%%JAVAJARDIR%%/igv/genomes/NC_001405.chrom.sizes
		64	%%JAVAJARDIR%%/igv/genomes/NC_001422.chrom.sizes
65	%%JAVAJARDIR%%/igv/genomes/NC_001623.chrom.sizes
66	%%JAVAJARDIR%%/igv/genomes/NC_001722.chrom.sizes
67	%%JAVAJARDIR%%/igv/genomes/NC_001802.chrom.sizes
68	%%JAVAJARDIR%%/igv/genomes/NC_002655.2.chrom.sizes
69	%%JAVAJARDIR%%/igv/genomes/NC_002755.chrom.sizes
70	%%JAVAJARDIR%%/igv/genomes/NC_002929.chrom.sizes
71	%%JAVAJARDIR%%/igv/genomes/NC_003112.chrom.sizes
72	%%JAVAJARDIR%%/igv/genomes/NC_003116.chrom.sizes
73	%%JAVAJARDIR%%/igv/genomes/NC_004917.chrom.sizes
74	%%JAVAJARDIR%%/igv/genomes/NC_008601.chrom.sizes
75	%%JAVAJARDIR%%/igv/genomes/NC_008767.chrom.sizes
76	%%JAVAJARDIR%%/igv/genomes/NC_009012.chrom.sizes
77	%%JAVAJARDIR%%/igv/genomes/NC_009012_alias.tab
78	%%JAVAJARDIR%%/igv/genomes/NC_012920.chrom.sizes
79	%%JAVAJARDIR%%/igv/genomes/NC_016856.chrom.sizes
80	%%JAVAJARDIR%%/igv/genomes/O_Sativa_r6.chrom.sizes
81	%%JAVAJARDIR%%/igv/genomes/OryCun2.0.chrom.sizes
82	%%JAVAJARDIR%%/igv/genomes/Pf3D7_v9.0.chrom.sizes
83	%%JAVAJARDIR%%/igv/genomes/Pf3D7_v9.0_alias.tab
84	%%JAVAJARDIR%%/igv/genomes/PlasmoDB_24.chrom.sizes
85	%%JAVAJARDIR%%/igv/genomes/PlasmoDB_7.0.chrom.sizes
86	%%JAVAJARDIR%%/igv/genomes/PlasmoDB_8.2.chrom.sizes
87	%%JAVAJARDIR%%/igv/genomes/Plasmodium_3D7_v2.1.chrom.sizes
88	%%JAVAJARDIR%%/igv/genomes/Plasmodium_3D7_v5.5.chrom.sizes
89	%%JAVAJARDIR%%/igv/genomes/Plasmodium_6.1.chrom.sizes
90	%%JAVAJARDIR%%/igv/genomes/SL2.31.chrom.sizes
91	%%JAVAJARDIR%%/igv/genomes/SL2.40.chrom.sizes
92	%%JAVAJARDIR%%/igv/genomes/U00096.2.chrom.sizes
93	%%JAVAJARDIR%%/igv/genomes/U00096.2_alias.tab
94	%%JAVAJARDIR%%/igv/genomes/VcholeraeN16961.chrom.sizes
95	%%JAVAJARDIR%%/igv/genomes/WS201.chrom.sizes
96	%%JAVAJARDIR%%/igv/genomes/WS220.chrom.sizes
97	%%JAVAJARDIR%%/igv/genomes/WS220_alias.tab
98	%%JAVAJARDIR%%/igv/genomes/WS245.chrom.sizes
99	%%JAVAJARDIR%%/igv/genomes/Y55.chrom.sizes
100	%%JAVAJARDIR%%/igv/genomes/ZmB73_5a.chrom.sizes
101	%%JAVAJARDIR%%/igv/genomes/ZmB73_5a_alias.tab
102	%%JAVAJARDIR%%/igv/genomes/anidulans_4.1.chrom.sizes
103	%%JAVAJARDIR%%/igv/genomes/anidulans_4.1_alias.tab
104	%%JAVAJARDIR%%/igv/genomes/b37.chrom.sizes
105	%%JAVAJARDIR%%/igv/genomes/b37_alias.tab
106	%%JAVAJARDIR%%/igv/genomes/bosTau3.chrom.sizes
107	%%JAVAJARDIR%%/igv/genomes/bosTau3_alias.tab
108	%%JAVAJARDIR%%/igv/genomes/bosTau4.chrom.sizes
109	%%JAVAJARDIR%%/igv/genomes/bosTau4_alias.tab
110	%%JAVAJARDIR%%/igv/genomes/bosTau6.chrom.sizes
111	%%JAVAJARDIR%%/igv/genomes/bosTau6_alias.tab
112	%%JAVAJARDIR%%/igv/genomes/bosTau7.chrom.sizes
113	%%JAVAJARDIR%%/igv/genomes/bosTau7_alias.tab
114	%%JAVAJARDIR%%/igv/genomes/bosTau8.chrom.sizes
115	%%JAVAJARDIR%%/igv/genomes/ca21.chrom.sizes
116	%%JAVAJARDIR%%/igv/genomes/canFam2.chrom.sizes
117	%%JAVAJARDIR%%/igv/genomes/canFam3.chrom.sizes
118	%%JAVAJARDIR%%/igv/genomes/candida.chrom.sizes
119	%%JAVAJARDIR%%/igv/genomes/cavPor3.chrom.sizes
120	%%JAVAJARDIR%%/igv/genomes/ce10.chrom.sizes
121	%%JAVAJARDIR%%/igv/genomes/ce11.chrom.sizes
122	%%JAVAJARDIR%%/igv/genomes/ce4.chrom.sizes
123	%%JAVAJARDIR%%/igv/genomes/ce6.chrom.sizes
124	%%JAVAJARDIR%%/igv/genomes/danRer10.chrom.sizes
125	%%JAVAJARDIR%%/igv/genomes/danRer11.chrom.sizes
126	%%JAVAJARDIR%%/igv/genomes/danRer6.chrom.sizes
127	%%JAVAJARDIR%%/igv/genomes/danRer7.chrom.sizes
128	%%JAVAJARDIR%%/igv/genomes/dm2.chrom.sizes
129	%%JAVAJARDIR%%/igv/genomes/dm3.chrom.sizes
130	%%JAVAJARDIR%%/igv/genomes/dm6.chrom.sizes
131	%%JAVAJARDIR%%/igv/genomes/dmel_5.9.chrom.sizes
132	%%JAVAJARDIR%%/igv/genomes/dmel_r5.22.chrom.sizes
133	%%JAVAJARDIR%%/igv/genomes/dmel_r5.33.chrom.sizes
134	%%JAVAJARDIR%%/igv/genomes/equCab2.chrom.sizes
135	%%JAVAJARDIR%%/igv/genomes/felCat5.chrom.sizes
136	%%JAVAJARDIR%%/igv/genomes/galGal3.chrom.sizes
137	%%JAVAJARDIR%%/igv/genomes/galGal4.chrom.sizes
138	%%JAVAJARDIR%%/igv/genomes/galGal5.chrom.sizes
139	%%JAVAJARDIR%%/igv/genomes/gasAcu1.chrom.sizes
140	%%JAVAJARDIR%%/igv/genomes/gmax10.chrom.sizes
141	%%JAVAJARDIR%%/igv/genomes/gmax8.chrom.sizes
142	%%JAVAJARDIR%%/igv/genomes/hg16.chrom.sizes
143	%%JAVAJARDIR%%/igv/genomes/hg17.chrom.sizes
144	%%JAVAJARDIR%%/igv/genomes/hg18.chrom.sizes
145	%%JAVAJARDIR%%/igv/genomes/hg19.chrom.sizes
146	%%JAVAJARDIR%%/igv/genomes/hg19_alias.tab
147	%%JAVAJARDIR%%/igv/genomes/hg38.chrom.sizes
148	%%JAVAJARDIR%%/igv/genomes/laevis_7.1.chrom.sizes
149	%%JAVAJARDIR%%/igv/genomes/lmjr.chrom.sizes
150	%%JAVAJARDIR%%/igv/genomes/lmjr_4.0.chrom.sizes
151	%%JAVAJARDIR%%/igv/genomes/lmjr_4.0_alias.tab
152	%%JAVAJARDIR%%/igv/genomes/me49.chrom.sizes
153	%%JAVAJARDIR%%/igv/genomes/mg8.chrom.sizes
154	%%JAVAJARDIR%%/igv/genomes/mm10.chrom.sizes
155	%%JAVAJARDIR%%/igv/genomes/mm7.chrom.sizes
156	%%JAVAJARDIR%%/igv/genomes/mm8.chrom.sizes
157	%%JAVAJARDIR%%/igv/genomes/mm9.chrom.sizes
158	%%JAVAJARDIR%%/igv/genomes/monDom5.chrom.sizes
159	%%JAVAJARDIR%%/igv/genomes/nc10.chrom.sizes
160	%%JAVAJARDIR%%/igv/genomes/nc10_alias.tab
161	%%JAVAJARDIR%%/igv/genomes/ncrassa_v3.chrom.sizes
162	%%JAVAJARDIR%%/igv/genomes/osativa_6.1.chrom.sizes
163	%%JAVAJARDIR%%/igv/genomes/osativa_6.1_alias.tab
164	%%JAVAJARDIR%%/igv/genomes/osativa_7.chrom.sizes
165	%%JAVAJARDIR%%/igv/genomes/oviAri3.chrom.sizes
166	%%JAVAJARDIR%%/igv/genomes/panTro2.chrom.sizes
167	%%JAVAJARDIR%%/igv/genomes/panTro3.chrom.sizes
168	%%JAVAJARDIR%%/igv/genomes/panTro4.chrom.sizes
169	%%JAVAJARDIR%%/igv/genomes/ppatens_1.2.chrom.sizes
170	%%JAVAJARDIR%%/igv/genomes/pvivax.chrom.sizes
171	%%JAVAJARDIR%%/igv/genomes/pvivax_alias.tab
172	%%JAVAJARDIR%%/igv/genomes/rheMac2.chrom.sizes
173	%%JAVAJARDIR%%/igv/genomes/rheMac3.chrom.sizes
174	%%JAVAJARDIR%%/igv/genomes/rheMac8.chrom.sizes
175	%%JAVAJARDIR%%/igv/genomes/rn4.chrom.sizes
176	%%JAVAJARDIR%%/igv/genomes/rn5.chrom.sizes
177	%%JAVAJARDIR%%/igv/genomes/rn6.chrom.sizes
178	%%JAVAJARDIR%%/igv/genomes/sacCer1.chrom.sizes
179	%%JAVAJARDIR%%/igv/genomes/sacCer2.chrom.sizes
180	%%JAVAJARDIR%%/igv/genomes/sacCer2_alias.tab
181	%%JAVAJARDIR%%/igv/genomes/sacCer3.chrom.sizes
182	%%JAVAJARDIR%%/igv/genomes/sacCer3_alias.tab
183	%%JAVAJARDIR%%/igv/genomes/sacCer62.chrom.sizes
184	%%JAVAJARDIR%%/igv/genomes/sacCer62_alias.tab
185	%%JAVAJARDIR%%/igv/genomes/sclerotiorum.chrom.sizes
186	%%JAVAJARDIR%%/igv/genomes/sk1.chrom.sizes
187	%%JAVAJARDIR%%/igv/genomes/spombe_1.55.chrom.sizes
188	%%JAVAJARDIR%%/igv/genomes/spombe_709.chrom.sizes
189	%%JAVAJARDIR%%/igv/genomes/spur_2.1.chrom.sizes
190	%%JAVAJARDIR%%/igv/genomes/spur_2.5.chrom.sizes
191	%%JAVAJARDIR%%/igv/genomes/spur_3.0.chrom.sizes
192	%%JAVAJARDIR%%/igv/genomes/susScr3.chrom.sizes
193	%%JAVAJARDIR%%/igv/genomes/susScrofa.chrom.sizes
194	%%JAVAJARDIR%%/igv/genomes/taeGut1.chrom.sizes
195	%%JAVAJARDIR%%/igv/genomes/tair10.chrom.sizes
196	%%JAVAJARDIR%%/igv/genomes/tair10_alias.tab
197	%%JAVAJARDIR%%/igv/genomes/tair8.chrom.sizes
198	%%JAVAJARDIR%%/igv/genomes/tair9.chrom.sizes
199	%%JAVAJARDIR%%/igv/genomes/tb427_4.2.chrom.sizes
200	%%JAVAJARDIR%%/igv/genomes/tb927.chrom.sizes
201	%%JAVAJARDIR%%/igv/genomes/tbgambi.chrom.sizes
202	%%JAVAJARDIR%%/igv/genomes/tbgambi_4.0.chrom.sizes
203	%%JAVAJARDIR%%/igv/genomes/tbgambi_4.0_alias.tab
204	%%JAVAJARDIR%%/igv/genomes/tbrucei927_4.0.chrom.sizes
205	%%JAVAJARDIR%%/igv/genomes/tbrucei927_4.0_alias.tab
206	%%JAVAJARDIR%%/igv/genomes/tbrucei927_5.0.chrom.sizes
207	%%JAVAJARDIR%%/igv/genomes/tcas_2.0.chrom.sizes
208	%%JAVAJARDIR%%/igv/genomes/tcas_3.0.chrom.sizes
209	%%JAVAJARDIR%%/igv/genomes/vvinifera.chrom.sizes
210	%%JAVAJARDIR%%/igv/genomes/ws241.chrom.sizes
211	%%JAVAJARDIR%%/igv/genomes/xenTro2.chrom.sizes
212	%%JAVAJARDIR%%/igv/genomes/xenTro9.chrom.sizes
213	%%JAVAJARDIR%%/igv/genomes/zebrafish.chrom.sizes
214	%%JAVAJARDIR%%/igv/goby-io-3.3.1.jar
215	%%JAVAJARDIR%%/igv/gson-2.8.5.jar
216	%%JAVAJARDIR%%/igv/guava-27.0.1-jre.jar
217	%%JAVAJARDIR%%/igv/htsjdk-2.23.0.jar
218	%%JAVAJARDIR%%/igv/http-client-spi-2.8.5.jar
219	%%JAVAJARDIR%%/igv/httpclient-4.5.9.jar
220	%%JAVAJARDIR%%/igv/httpcore-4.4.11.jar
221	%%JAVAJARDIR%%/igv/icb-utils-2.0.2.jar
222	%%JAVAJARDIR%%/igv/igv.args
223	%%JAVAJARDIR%%/igv/igv.jar
224	%%JAVAJARDIR%%/igv/j2objc-annotations-1.1.jar
225	%%JAVAJARDIR%%/igv/jackson-annotations-2.9.0.jar
226	%%JAVAJARDIR%%/igv/jackson-core-2.9.8.jar
227	%%JAVAJARDIR%%/igv/jackson-databind-2.9.8.jar
228	%%JAVAJARDIR%%/igv/jide-common-3.7.3.jar
229	%%JAVAJARDIR%%/igv/jsap-3.0.0.jar
230	%%JAVAJARDIR%%/igv/log4j-1.2-api-2.11.0.jar
231	%%JAVAJARDIR%%/igv/log4j-api-2.11.0.jar
232	%%JAVAJARDIR%%/igv/log4j-core-2.11.0.jar
233	%%JAVAJARDIR%%/igv/netty-buffer-4.1.39.Final.jar
234	%%JAVAJARDIR%%/igv/netty-codec-4.1.39.Final.jar
235	%%JAVAJARDIR%%/igv/netty-codec-http-4.1.39.Final.jar
236	%%JAVAJARDIR%%/igv/netty-common-4.1.39.Final.jar
237	%%JAVAJARDIR%%/igv/netty-handler-4.1.39.Final.jar
238	%%JAVAJARDIR%%/igv/netty-nio-client-2.8.5.jar
239	%%JAVAJARDIR%%/igv/netty-reactive-streams-2.0.3.jar
240	%%JAVAJARDIR%%/igv/netty-reactive-streams-http-2.0.3.jar
241	%%JAVAJARDIR%%/igv/netty-resolver-4.1.39.Final.jar
242	%%JAVAJARDIR%%/igv/netty-transport-4.1.39.Final.jar
243	%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.39.Final-linux-x86_64.jar
244	%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.39.Final.jar
245	%%JAVAJARDIR%%/igv/ngs-java-2.9.0.jar
246	%%JAVAJARDIR%%/igv/profiles-2.8.5.jar
247	%%JAVAJARDIR%%/igv/protobuf-java-3.7.0-rc1.jar
248	%%JAVAJARDIR%%/igv/protocol-core-2.8.5.jar
249	%%JAVAJARDIR%%/igv/reactive-streams-1.0.2.jar
250	%%JAVAJARDIR%%/igv/regions-2.8.5.jar
251	%%JAVAJARDIR%%/igv/s3-2.8.5.jar
252	%%JAVAJARDIR%%/igv/sdk-core-2.8.5.jar
253	%%JAVAJARDIR%%/igv/slf4j-api-1.7.26.jar
254	%%JAVAJARDIR%%/igv/slf4j-simple-1.7.26.jar
255	%%JAVAJARDIR%%/igv/snappy-java-1.1.7.3.jar
256	%%JAVAJARDIR%%/igv/sts-2.8.5.jar
257	%%JAVAJARDIR%%/igv/swing-layout-1.0.3.jar
258	%%JAVAJARDIR%%/igv/utils-2.8.5.jar
259	%%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar
260	share/pixmaps/igv.png