svn commit: r473356 - in head/biology: . igv igv/files

[Yuri Victorovich]

Author: yuri
Date: Mon Jun 25 23:56:00 2018
New Revision: 473356
URL: https://svnweb.freebsd.org/changeset/ports/473356

Log:
  New port: biology/igv: Visualization tool for genomic datasets

Added:
  head/biology/igv/
  head/biology/igv/Makefile   (contents, props changed)
  head/biology/igv/distinfo   (contents, props changed)
  head/biology/igv/files/
  head/biology/igv/files/igv.sh.in   (contents, props changed)
  head/biology/igv/files/patch-build.xml   (contents, props changed)
  head/biology/igv/pkg-descr   (contents, props changed)
Modified:
  head/biology/Makefile

Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile	Mon Jun 25 23:36:59 2018	(r473355)
+++ head/biology/Makefile	Mon Jun 25 23:56:00 2018	(r473356)
@@ -43,6 +43,7 @@
     SUBDIR += hmmer
     SUBDIR += htslib
     SUBDIR += hyphy
+    SUBDIR += igv
     SUBDIR += infernal
     SUBDIR += iolib
     SUBDIR += iqtree

Added: head/biology/igv/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/igv/Makefile	Mon Jun 25 23:56:00 2018	(r473356)
@@ -0,0 +1,46 @@
+# $FreeBSD$
+
+PORTNAME=	igv
+DISTVERSIONPREFIX=	v
+DISTVERSION=	2.4.10
+CATEGORIES=	biology java
+MASTER_SITES=	http://www.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img
+DISTFILES=	tools.png:img
+DIST_SUBDIR=	${PORTNAME}-${DISTVERSION}
+EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
+
+MAINTAINER=	yuri at FreeBSD.org
+COMMENT=	Visualization tool for genomic datasets
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/license.txt
+
+BUILD_DEPENDS=	openjfx8-devel>0:java/openjfx8-devel
+RUN_DEPENDS=	openjfx8-devel>0:java/openjfx8-devel
+
+USES=		gettext-runtime
+USE_GITHUB=	yes
+GH_ACCOUNT=	igvteam
+USE_JAVA=	yes
+USE_ANT=	yes
+NO_ARCH=	yes
+
+SUB_FILES=	${PORTNAME}.sh
+
+DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \
+		"Biology;Science;" true
+
+PLIST_FILES=	bin/${PORTNAME} \
+		${JAVAJARDIR}/batik-codec__V1.7.jar \
+		${JAVAJARDIR}/goby-io-igv__V1.0.jar \
+		${JAVAJARDIR}/${PORTNAME}.jar \
+		share/pixmaps/igv.png
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME}.sh ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
+	${INSTALL_DATA} ${WRKSRC}/${PORTNAME}.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/batik-codec__V1.7.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${WRKSRC}/goby-io-igv__V1.0.jar ${STAGEDIR}${JAVAJARDIR}
+	${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/tools.png ${STAGEDIR}${PREFIX}/share/pixmaps/${PORTNAME}.png
+
+.include <bsd.port.mk>

Added: head/biology/igv/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/igv/distinfo	Mon Jun 25 23:56:00 2018	(r473356)
@@ -0,0 +1,5 @@
+TIMESTAMP = 1529969906
+SHA256 (igv-2.4.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c
+SIZE (igv-2.4.10/tools.png) = 5139
+SHA256 (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 2547050f768384ea14f88962476c6935115e6b2e35322874e4a93c6da7194e73
+SIZE (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 152822902

Added: head/biology/igv/files/igv.sh.in
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/igv/files/igv.sh.in	Mon Jun 25 23:56:00 2018	(r473356)
@@ -0,0 +1,9 @@
+#!/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

Added: head/biology/igv/files/patch-build.xml
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/igv/files/patch-build.xml	Mon Jun 25 23:56:00 2018	(r473356)
@@ -0,0 +1,10 @@
+--- build.xml.orig	2018-06-25 21:00:29 UTC
++++ build.xml
+@@ -177,6 +177,7 @@
+         <sequential>
+             <jar destfile="${jar.path}" basedir="${tmp.dir}" compress="true" duplicate="preserve">
+                 <fileset refid="@{includedFileset}"/>
++                <zipgroupfileset dir="${lib.dir}" includes="**/*.jar" />
+                 <manifest>
+ 
+                     <attribute name="Permissions" value="all-permissions"/>

Added: head/biology/igv/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/igv/pkg-descr	Mon Jun 25 23:56:00 2018	(r473356)
@@ -0,0 +1,6 @@
+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.
+
+WWW: https://software.broadinstitute.org/software/igv/