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

[bacon <bacon%pkgsrc.org@localhost>]

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
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+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
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