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.

5 files changed, 343 insertions, 0 deletions

diff --git a/biology/igv/DESCR b/biology/igv/DESCR
new file mode 100644
index 00000000000..c3c10e11e26
--- /dev/null
+++ b/biology/igv/DESCR
@@ -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 --git a/biology/igv/Makefile b/biology/igv/Makefile
new file mode 100644
index 00000000000..0964f1d0b67
--- /dev/null
+++ b/biology/igv/Makefile
@@ -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
+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 --git a/biology/igv/PLIST b/biology/igv/PLIST
new file mode 100644
index 00000000000..3326ef91631
--- /dev/null
+++ b/biology/igv/PLIST
@@ -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
+share/java/classes/igv/genomes/NC_000913.2_alias.tab
+share/java/classes/igv/genomes/NC_000913.chrom.sizes
+share/java/classes/igv/genomes/NC_000964.chrom.sizes
+share/java/classes/igv/genomes/NC_001405.chrom.sizes
+share/java/classes/igv/genomes/NC_001422.chrom.sizes
+share/java/classes/igv/genomes/NC_001623.chrom.sizes
+share/java/classes/igv/genomes/NC_001722.chrom.sizes
+share/java/classes/igv/genomes/NC_001802.chrom.sizes
+share/java/classes/igv/genomes/NC_002655.2.chrom.sizes
+share/java/classes/igv/genomes/NC_002755.chrom.sizes
+share/java/classes/igv/genomes/NC_002929.chrom.sizes
+share/java/classes/igv/genomes/NC_003112.chrom.sizes
+share/java/classes/igv/genomes/NC_003116.chrom.sizes
+share/java/classes/igv/genomes/NC_004917.chrom.sizes
+share/java/classes/igv/genomes/NC_008601.chrom.sizes
+share/java/classes/igv/genomes/NC_008767.chrom.sizes
+share/java/classes/igv/genomes/NC_009012.chrom.sizes
+share/java/classes/igv/genomes/NC_009012_alias.tab
+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
+share/java/classes/igv/genomes/anidulans_4.1.chrom.sizes
+share/java/classes/igv/genomes/anidulans_4.1_alias.tab
+share/java/classes/igv/genomes/b37.chrom.sizes
+share/java/classes/igv/genomes/b37_alias.tab
+share/java/classes/igv/genomes/bosTau3.chrom.sizes
+share/java/classes/igv/genomes/bosTau3_alias.tab
+share/java/classes/igv/genomes/bosTau4.chrom.sizes
+share/java/classes/igv/genomes/bosTau4_alias.tab
+share/java/classes/igv/genomes/bosTau6.chrom.sizes
+share/java/classes/igv/genomes/bosTau6_alias.tab
+share/java/classes/igv/genomes/bosTau7.chrom.sizes
+share/java/classes/igv/genomes/bosTau7_alias.tab
+share/java/classes/igv/genomes/bosTau8.chrom.sizes
+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
+share/java/classes/igv/genomes/lmjr_4.0_alias.tab
+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
+share/java/classes/igv/genomes/sacCer1.chrom.sizes
+share/java/classes/igv/genomes/sacCer2.chrom.sizes
+share/java/classes/igv/genomes/sacCer2_alias.tab
+share/java/classes/igv/genomes/sacCer3.chrom.sizes
+share/java/classes/igv/genomes/sacCer3_alias.tab
+share/java/classes/igv/genomes/sacCer62.chrom.sizes
+share/java/classes/igv/genomes/sacCer62_alias.tab
+share/java/classes/igv/genomes/sclerotiorum.chrom.sizes
+share/java/classes/igv/genomes/sk1.chrom.sizes
+share/java/classes/igv/genomes/spombe_1.55.chrom.sizes
+share/java/classes/igv/genomes/spombe_709.chrom.sizes
+share/java/classes/igv/genomes/spur_2.1.chrom.sizes
+share/java/classes/igv/genomes/spur_2.5.chrom.sizes
+share/java/classes/igv/genomes/spur_3.0.chrom.sizes
+share/java/classes/igv/genomes/susScr3.chrom.sizes
+share/java/classes/igv/genomes/susScrofa.chrom.sizes
+share/java/classes/igv/genomes/taeGut1.chrom.sizes
+share/java/classes/igv/genomes/tair10.chrom.sizes
+share/java/classes/igv/genomes/tair10_alias.tab
+share/java/classes/igv/genomes/tair8.chrom.sizes
+share/java/classes/igv/genomes/tair9.chrom.sizes
+share/java/classes/igv/genomes/tb427_4.2.chrom.sizes
+share/java/classes/igv/genomes/tb927.chrom.sizes
+share/java/classes/igv/genomes/tbgambi.chrom.sizes
+share/java/classes/igv/genomes/tbgambi_4.0.chrom.sizes
+share/java/classes/igv/genomes/tbgambi_4.0_alias.tab
+share/java/classes/igv/genomes/tbrucei927_4.0.chrom.sizes
+share/java/classes/igv/genomes/tbrucei927_4.0_alias.tab
+share/java/classes/igv/genomes/tbrucei927_5.0.chrom.sizes
+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
+share/java/classes/igv/goby-io-3.3.1.jar
+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
+share/java/classes/igv/log4j-1.2-api-2.11.0.jar
+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
+share/java/classes/igv/netty-nio-client-2.15.67.jar
+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
+share/java/classes/igv/netty-transport-native-epoll-4.1.53.Final-linux-x86_64.jar
+share/java/classes/igv/netty-transport-native-unix-common-4.1.53.Final.jar
+share/java/classes/igv/ngs-java-2.9.0.jar
+share/java/classes/igv/profiles-2.15.67.jar
+share/java/classes/igv/protobuf-java-3.7.0-rc1.jar
+share/java/classes/igv/protocol-core-2.15.67.jar
+share/java/classes/igv/reactive-streams-1.0.3.jar
+share/java/classes/igv/regions-2.15.67.jar
+share/java/classes/igv/s3-2.15.67.jar
+share/java/classes/igv/sdk-core-2.15.67.jar
+share/java/classes/igv/slf4j-api-1.7.28.jar
+share/java/classes/igv/slf4j-simple-1.7.26.jar
+share/java/classes/igv/snappy-java-1.1.7.3.jar
+share/java/classes/igv/sts-2.15.67.jar
+share/java/classes/igv/swing-layout-1.0.3.jar
+share/java/classes/igv/utils-2.15.67.jar
+share/java/classes/igv/xmlgraphics-commons-2.3.jar
diff --git a/biology/igv/distinfo b/biology/igv/distinfo
new file mode 100644
index 00000000000..268dad5516b
--- /dev/null
+++ b/biology/igv/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2021/02/24 13:54:25 bacon Exp $
+
+SHA1 (IGV_2.9.2.zip) = 873b273f25b757f4f808fff690b0d4d0f55dea39
+RMD160 (IGV_2.9.2.zip) = 1f44e603d55cee22a64eedbb874b75f6efa77835
+SHA512 (IGV_2.9.2.zip) = 6c8156401b0ba760f59b50a8004dcd025d0f6ac6a86776a6928af857c6d4309c914d2552fdde0dd89eddf443d7e18ab7b0fa9db15737701815cf3190a78b4c30
+Size (IGV_2.9.2.zip) = 55890979 bytes
diff --git a/biology/igv/files/igv.sh.in b/biology/igv/files/igv.sh.in
new file mode 100755
index 00000000000..0b87c996d43
--- /dev/null
+++ b/biology/igv/files/igv.sh.in
@@ -0,0 +1,32 @@
+#!/bin/sh
+
+if [ -e /usr/libexec/java_home ]; then
+    # MacOS openjdk
+    export JAVA_HOME=$(/usr/libexec/java_home)
+elif [ -e %%PREFIX%%/java/openjdk11/bin/java ]; then
+    # Custom pkgsrc
+    export JAVA_HOME=%%PREFIX%%/java/openjdk11
+elif [ -e /usr/pkg/java/openjdk11/bin/java ]; then
+    # Try NetBSD default pkgsrc if not installed in the custom tree
+    export JAVA_HOME=/usr/pkg/java/openjdk11
+fi
+
+if [ -e $JAVA_HOME/bin/java ]; then
+    java=$JAVA_HOME/bin/java
+else
+    # Assume env is correctly configured
+    java=java
+fi
+
+if ! $java -version 2>&1 | head -n 1 | fgrep '"11.'; then
+    printf "You need Java 11 to run IGV.\n"
+    java -version
+    exit 1
+fi
+
+$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 "$@"