diff options
| author | Yuri Victorovich <yuri@FreeBSD.org> | 2018-06-25 23:56:00 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2018-06-25 23:56:00 +0000 |
| commit | 77640f32a7378138bb4aa42f42c1bb8bf5490f2a (patch) | |
| tree | 9df14b69decaec881f863a89911ea99a176bd1a8 /biology | |
| parent | Mark as broken on -CURRENT. (diff) | |
New port: biology/igv: Visualization tool for genomic datasets
Notes
Notes:
svn path=/head/; revision=473356
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/igv/Makefile | 46 | ||||
| -rw-r--r-- | biology/igv/distinfo | 5 | ||||
| -rw-r--r-- | biology/igv/files/igv.sh.in | 9 | ||||
| -rw-r--r-- | biology/igv/files/patch-build.xml | 10 | ||||
| -rw-r--r-- | biology/igv/pkg-descr | 6 |
6 files changed, 77 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 23491064e01d..e83a480b7974 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -43,6 +43,7 @@ SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy + SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree diff --git a/biology/igv/Makefile b/biology/igv/Makefile new file mode 100644 index 000000000000..367c84948ab8 --- /dev/null +++ b/biology/igv/Makefile @@ -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@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/${PORTNAME}.png + +.include <bsd.port.mk> diff --git a/biology/igv/distinfo b/biology/igv/distinfo new file mode 100644 index 000000000000..76f41bfff53b --- /dev/null +++ b/biology/igv/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1529969906 +SHA256 (igv-2.4.10/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.4.10/tools.png) = 5139 +SHA256 (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 2547050f768384ea14f88962476c6935115e6b2e35322874e4a93c6da7194e73 +SIZE (igv-2.4.10/igvteam-igv-v2.4.10_GH0.tar.gz) = 152822902 diff --git a/biology/igv/files/igv.sh.in b/biology/igv/files/igv.sh.in new file mode 100644 index 000000000000..ab2df746a8e5 --- /dev/null +++ b/biology/igv/files/igv.sh.in @@ -0,0 +1,9 @@ +#!/bin/sh +LANG=C +# phymem=$(free -m | awk '/^Mem:/{print $2}') +#igvmem=$(($phymem / 3)) +# ARGS=-Xmx${igvmem}m +java $ARGS \ + -Dapple.laf.useScreenMenuBar=true \ + -Djava.net.preferIPv4Stack=true \ + -jar %%JAVAJARDIR%%/igv.jar diff --git a/biology/igv/files/patch-build.xml b/biology/igv/files/patch-build.xml new file mode 100644 index 000000000000..b65970df3df9 --- /dev/null +++ b/biology/igv/files/patch-build.xml @@ -0,0 +1,10 @@ +--- build.xml.orig 2018-06-25 21:00:29 UTC ++++ build.xml +@@ -177,6 +177,7 @@ + <sequential> + <jar destfile="${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"/> diff --git a/biology/igv/pkg-descr b/biology/igv/pkg-descr new file mode 100644 index 000000000000..9a9d574c4838 --- /dev/null +++ b/biology/igv/pkg-descr @@ -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/ |