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[pkgsrc/trunk]: pkgsrc/biology/igv biology/igv: import igv-2.9.2



details:   https://anonhg.NetBSD.org/pkgsrc/rev/fcf79a277275
branches:  trunk
changeset: 447654:fcf79a277275
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Wed Feb 24 13:54:25 2021 +0000

description:
biology/igv: import igv-2.9.2

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool
for interactive exploration of large, integrated genomic datasets. It supports
a wide variety of data types, including array-based and next-generation
sequence data, and genomic annotations.

diffstat:

 biology/igv/DESCR           |    4 +
 biology/igv/Makefile        |   37 ++++++
 biology/igv/PLIST           |  264 ++++++++++++++++++++++++++++++++++++++++++++
 biology/igv/distinfo        |    6 +
 biology/igv/files/igv.sh.in |   32 +++++
 5 files changed, 343 insertions(+), 0 deletions(-)

diffs (truncated from 363 to 300 lines):

diff -r 1240467006d0 -r fcf79a277275 biology/igv/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/igv/DESCR Wed Feb 24 13:54:25 2021 +0000
@@ -0,0 +1,4 @@
+The Integrative Genomics Viewer (IGV) is a high-performance visualization tool
+for interactive exploration of large, integrated genomic datasets. It supports
+a wide variety of data types, including array-based and next-generation
+sequence data, and genomic annotations.
diff -r 1240467006d0 -r fcf79a277275 biology/igv/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/igv/Makefile      Wed Feb 24 13:54:25 2021 +0000
@@ -0,0 +1,37 @@
+# $NetBSD: Makefile,v 1.1 2021/02/24 13:54:25 bacon Exp $
+
+DISTNAME=      IGV_2.9.2
+PKGNAME=       ${DISTNAME:S/IGV_/igv-/}
+CATEGORIES=    biology
+MASTER_SITES=  https://data.broadinstitute.org/igv/projects/downloads/${PKGVERSION_NOREV:R}/
+EXTRACT_SUFX=  .zip
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      https://software.broadinstitute.org/software/igv/
+COMMENT=       Visualization tool for genomic datasets
+LICENSE=       mit
+
+USE_JAVA=      yes
+USE_JAVA2=     9       # Actually needs 11, not supported by java-vm.mk
+USE_TOOLS+=    pax
+NO_BUILD=      yes
+
+SUBST_CLASSES+=                java
+SUBST_STAGE.java=      pre-configure
+SUBST_SED.java=                -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
+SUBST_SED.java+=       -e 's|%%PREFIX%%|${PREFIX}|g'
+SUBST_FILES.java=      igv
+
+JAVAJARDIR=            ${PREFIX}/share/java/classes
+INSTALLATION_DIRS=     bin ${JAVAJARDIR}/igv
+
+pre-patch:
+       ${CP} ${FILESDIR}/igv.sh.in ${WRKSRC}/igv
+
+do-install:
+       ${INSTALL_SCRIPT} ${WRKSRC}/igv ${DESTDIR}${PREFIX}/bin
+       ${INSTALL_DATA} ${WRKSRC}/lib/*.jar ${DESTDIR}${JAVAJARDIR}/igv
+       ${INSTALL_DATA} ${WRKSRC}/igv.args ${DESTDIR}${JAVAJARDIR}/igv
+       cd ${WRKSRC}/lib && pax -rw genomes ${DESTDIR}${JAVAJARDIR}/igv
+
+.include "../../mk/bsd.pkg.mk"
diff -r 1240467006d0 -r fcf79a277275 biology/igv/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/igv/PLIST Wed Feb 24 13:54:25 2021 +0000
@@ -0,0 +1,264 @@
+@comment $NetBSD: PLIST,v 1.1 2021/02/24 13:54:25 bacon Exp $
+bin/igv
+share/java/classes/igv/AbsoluteLayout-RELEASE110.jar
+share/java/classes/igv/annotations-2.15.67.jar
+share/java/classes/igv/apache-client-2.15.67.jar
+share/java/classes/igv/arns-2.15.67.jar
+share/java/classes/igv/auth-2.15.67.jar
+share/java/classes/igv/aws-core-2.15.67.jar
+share/java/classes/igv/aws-json-protocol-2.15.67.jar
+share/java/classes/igv/aws-query-protocol-2.15.67.jar
+share/java/classes/igv/aws-xml-protocol-2.15.67.jar
+share/java/classes/igv/batik-awt-util-1.11.jar
+share/java/classes/igv/batik-codec-1.11.jar
+share/java/classes/igv/batik-constants-1.11.jar
+share/java/classes/igv/batik-dom-1.11.jar
+share/java/classes/igv/batik-ext-1.11.jar
+share/java/classes/igv/batik-i18n-1.11.jar
+share/java/classes/igv/batik-svggen-1.11.jar
+share/java/classes/igv/batik-transcoder-1.11.jar
+share/java/classes/igv/batik-util-1.11.jar
+share/java/classes/igv/batik-xml-1.11.jar
+share/java/classes/igv/cognitoidentity-2.15.67.jar
+share/java/classes/igv/commons-codec-1.11.jar
+share/java/classes/igv/commons-collections-20040616.jar
+share/java/classes/igv/commons-compress-1.19.jar
+share/java/classes/igv/commons-configuration-1.10.jar
+share/java/classes/igv/commons-io-2.6.jar
+share/java/classes/igv/commons-jexl-2.1.1.jar
+share/java/classes/igv/commons-lang-2.6.jar
+share/java/classes/igv/commons-lang3-3.9.jar
+share/java/classes/igv/commons-logging-1.2.jar
+share/java/classes/igv/commons-math3-3.6.1.jar
+share/java/classes/igv/dsiutils-2.3.3.jar
+share/java/classes/igv/eventstream-1.0.1.jar
+share/java/classes/igv/fastutil-7.0.12.jar
+share/java/classes/igv/genomes/1kg_ref.chrom.sizes
+share/java/classes/igv/genomes/1kg_v37.chrom.sizes
+share/java/classes/igv/genomes/1kg_v37_alias.tab
+share/java/classes/igv/genomes/ABaumannii_ATCC_17978.chrom.sizes
+share/java/classes/igv/genomes/ABaumannii_AYE_uid61637.chrom.sizes
+share/java/classes/igv/genomes/AGPv3.31.chrom.sizes
+share/java/classes/igv/genomes/AgamP3.chrom.sizes
+share/java/classes/igv/genomes/Aplysia.chrom.sizes
+share/java/classes/igv/genomes/B73.chrom.sizes
+share/java/classes/igv/genomes/CCAF000000000.chrom.sizes
+share/java/classes/igv/genomes/CE_1.0.chrom.sizes
+share/java/classes/igv/genomes/CSavignyi_v2.1.chrom.sizes
+share/java/classes/igv/genomes/D.discoideum.chrom.sizes
+share/java/classes/igv/genomes/EBV_Type2.chrom.sizes
+share/java/classes/igv/genomes/Foxy4287.chrom.sizes
+share/java/classes/igv/genomes/GCF_000233375.1.chrom.sizes
+share/java/classes/igv/genomes/GSM552910.chrom.sizes
+share/java/classes/igv/genomes/GSM552910_alias.tab
+share/java/classes/igv/genomes/Glamblia_2.0.chrom.sizes
+share/java/classes/igv/genomes/HHV4_Type1.chrom.sizes
+share/java/classes/igv/genomes/ITAG2.3.chrom.sizes
+share/java/classes/igv/genomes/ITAG2.3_alias.tab
+share/java/classes/igv/genomes/M74568.chrom.sizes
+share/java/classes/igv/genomes/MusPutFur1.0.chrom.sizes
+share/java/classes/igv/genomes/MusaAcuminata.chrom.sizes
+share/java/classes/igv/genomes/MusaBalbisianaPKWv1.chrom.sizes
+share/java/classes/igv/genomes/NC_000913.2.chrom.sizes
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+share/java/classes/igv/genomes/NC_002929.chrom.sizes
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+share/java/classes/igv/genomes/NC_012920.chrom.sizes
+share/java/classes/igv/genomes/NC_016856.chrom.sizes
+share/java/classes/igv/genomes/O_Sativa_r6.chrom.sizes
+share/java/classes/igv/genomes/OryCun2.0.chrom.sizes
+share/java/classes/igv/genomes/Pf3D7_v9.0.chrom.sizes
+share/java/classes/igv/genomes/Pf3D7_v9.0_alias.tab
+share/java/classes/igv/genomes/PlasmoDB_24.chrom.sizes
+share/java/classes/igv/genomes/PlasmoDB_7.0.chrom.sizes
+share/java/classes/igv/genomes/PlasmoDB_8.2.chrom.sizes
+share/java/classes/igv/genomes/Plasmodium_3D7_v2.1.chrom.sizes
+share/java/classes/igv/genomes/Plasmodium_3D7_v5.5.chrom.sizes
+share/java/classes/igv/genomes/Plasmodium_6.1.chrom.sizes
+share/java/classes/igv/genomes/SL2.31.chrom.sizes
+share/java/classes/igv/genomes/SL2.40.chrom.sizes
+share/java/classes/igv/genomes/U00096.2.chrom.sizes
+share/java/classes/igv/genomes/U00096.2_alias.tab
+share/java/classes/igv/genomes/VcholeraeN16961.chrom.sizes
+share/java/classes/igv/genomes/WS201.chrom.sizes
+share/java/classes/igv/genomes/WS220.chrom.sizes
+share/java/classes/igv/genomes/WS220_alias.tab
+share/java/classes/igv/genomes/WS245.chrom.sizes
+share/java/classes/igv/genomes/Y55.chrom.sizes
+share/java/classes/igv/genomes/ZmB73_5a.chrom.sizes
+share/java/classes/igv/genomes/ZmB73_5a_alias.tab
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+share/java/classes/igv/genomes/b37.chrom.sizes
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+share/java/classes/igv/genomes/ca21.chrom.sizes
+share/java/classes/igv/genomes/canFam2.chrom.sizes
+share/java/classes/igv/genomes/canFam3.chrom.sizes
+share/java/classes/igv/genomes/canFam4.chrom.sizes
+share/java/classes/igv/genomes/candida.chrom.sizes
+share/java/classes/igv/genomes/cavPor3.chrom.sizes
+share/java/classes/igv/genomes/ce10.chrom.sizes
+share/java/classes/igv/genomes/ce11.chrom.sizes
+share/java/classes/igv/genomes/ce4.chrom.sizes
+share/java/classes/igv/genomes/ce6.chrom.sizes
+share/java/classes/igv/genomes/danRer10.chrom.sizes
+share/java/classes/igv/genomes/danRer11.chrom.sizes
+share/java/classes/igv/genomes/danRer6.chrom.sizes
+share/java/classes/igv/genomes/danRer7.chrom.sizes
+share/java/classes/igv/genomes/dm2.chrom.sizes
+share/java/classes/igv/genomes/dm3.chrom.sizes
+share/java/classes/igv/genomes/dm6.chrom.sizes
+share/java/classes/igv/genomes/dmel_5.9.chrom.sizes
+share/java/classes/igv/genomes/dmel_r5.22.chrom.sizes
+share/java/classes/igv/genomes/dmel_r5.33.chrom.sizes
+share/java/classes/igv/genomes/equCab2.chrom.sizes
+share/java/classes/igv/genomes/felCat5.chrom.sizes
+share/java/classes/igv/genomes/galGal3.chrom.sizes
+share/java/classes/igv/genomes/galGal4.chrom.sizes
+share/java/classes/igv/genomes/galGal5.chrom.sizes
+share/java/classes/igv/genomes/gasAcu1.chrom.sizes
+share/java/classes/igv/genomes/gmax10.chrom.sizes
+share/java/classes/igv/genomes/gmax8.chrom.sizes
+share/java/classes/igv/genomes/hg16.chrom.sizes
+share/java/classes/igv/genomes/hg17.chrom.sizes
+share/java/classes/igv/genomes/hg18.chrom.sizes
+share/java/classes/igv/genomes/hg19.chrom.sizes
+share/java/classes/igv/genomes/hg19_alias.tab
+share/java/classes/igv/genomes/hg38.chrom.sizes
+share/java/classes/igv/genomes/laevis_7.1.chrom.sizes
+share/java/classes/igv/genomes/lmjr.chrom.sizes
+share/java/classes/igv/genomes/lmjr_4.0.chrom.sizes
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+share/java/classes/igv/genomes/me49.chrom.sizes
+share/java/classes/igv/genomes/mg8.chrom.sizes
+share/java/classes/igv/genomes/mm10.chrom.sizes
+share/java/classes/igv/genomes/mm7.chrom.sizes
+share/java/classes/igv/genomes/mm8.chrom.sizes
+share/java/classes/igv/genomes/mm9.chrom.sizes
+share/java/classes/igv/genomes/monDom5.chrom.sizes
+share/java/classes/igv/genomes/nc10.chrom.sizes
+share/java/classes/igv/genomes/nc10_alias.tab
+share/java/classes/igv/genomes/ncrassa_v3.chrom.sizes
+share/java/classes/igv/genomes/osativa_6.1.chrom.sizes
+share/java/classes/igv/genomes/osativa_6.1_alias.tab
+share/java/classes/igv/genomes/osativa_7.chrom.sizes
+share/java/classes/igv/genomes/oviAri3.chrom.sizes
+share/java/classes/igv/genomes/panTro2.chrom.sizes
+share/java/classes/igv/genomes/panTro3.chrom.sizes
+share/java/classes/igv/genomes/panTro4.chrom.sizes
+share/java/classes/igv/genomes/ppatens_1.2.chrom.sizes
+share/java/classes/igv/genomes/pvivax.chrom.sizes
+share/java/classes/igv/genomes/pvivax_alias.tab
+share/java/classes/igv/genomes/rheMac2.chrom.sizes
+share/java/classes/igv/genomes/rheMac3.chrom.sizes
+share/java/classes/igv/genomes/rheMac8.chrom.sizes
+share/java/classes/igv/genomes/rn4.chrom.sizes
+share/java/classes/igv/genomes/rn5.chrom.sizes
+share/java/classes/igv/genomes/rn6.chrom.sizes
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+share/java/classes/igv/genomes/susScrofa.chrom.sizes
+share/java/classes/igv/genomes/taeGut1.chrom.sizes
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+share/java/classes/igv/genomes/tb927.chrom.sizes
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+share/java/classes/igv/genomes/tcas_2.0.chrom.sizes
+share/java/classes/igv/genomes/tcas_3.0.chrom.sizes
+share/java/classes/igv/genomes/vvinifera.chrom.sizes
+share/java/classes/igv/genomes/ws241.chrom.sizes
+share/java/classes/igv/genomes/xenTro2.chrom.sizes
+share/java/classes/igv/genomes/xenTro9.chrom.sizes
+share/java/classes/igv/genomes/zebrafish.chrom.sizes
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+share/java/classes/igv/gson-2.8.5.jar
+share/java/classes/igv/guava-27.0.1-jre.jar
+share/java/classes/igv/htsjdk-2.23.0.jar
+share/java/classes/igv/http-client-spi-2.15.67.jar
+share/java/classes/igv/httpclient-4.5.13.jar
+share/java/classes/igv/httpcore-4.4.13.jar
+share/java/classes/igv/icb-utils-2.0.2.jar
+share/java/classes/igv/igv.args
+share/java/classes/igv/igv.jar
+share/java/classes/igv/j2objc-annotations-1.1.jar
+share/java/classes/igv/jackson-annotations-2.10.5.jar
+share/java/classes/igv/jackson-core-2.10.5.jar
+share/java/classes/igv/jackson-databind-2.10.5.1.jar
+share/java/classes/igv/jide-common-3.7.3.jar
+share/java/classes/igv/jsap-3.0.0.jar
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+share/java/classes/igv/log4j-api-2.11.0.jar
+share/java/classes/igv/log4j-core-2.11.0.jar
+share/java/classes/igv/metrics-spi-2.15.67.jar
+share/java/classes/igv/netty-buffer-4.1.53.Final.jar
+share/java/classes/igv/netty-codec-4.1.53.Final.jar
+share/java/classes/igv/netty-codec-http-4.1.53.Final.jar
+share/java/classes/igv/netty-common-4.1.53.Final.jar
+share/java/classes/igv/netty-handler-4.1.53.Final.jar
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+share/java/classes/igv/netty-reactive-streams-2.0.4.jar
+share/java/classes/igv/netty-reactive-streams-http-2.0.4.jar
+share/java/classes/igv/netty-resolver-4.1.53.Final.jar
+share/java/classes/igv/netty-transport-4.1.53.Final.jar



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