commit: b63f594da84935c8eb06d4102b8724f621c5e4fe Author: Johann Schmitz <johann <AT> j-schmitz <DOT> net> AuthorDate: Sat Mar 21 17:33:30 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sat Mar 21 17:33:30 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b63f594d
Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as requested by Martin Mokrejŝ (note: i've excluded the test code by passing -Dnotests=true to ant so it may break at some point). Also improved the ebuild by unbundling stuff we already have in portage. There are quite a number of libraries which aren't used for compilation which may be needed at runtime. I haven't tested the program in depth: it started at didn't throw errors when i clicked around - everything else is way beyond my knowledge. Improved the ebuild for sci-biology/igv Package-Manager: portage-2.2.14 sci-biology/igv/ChangeLog | 10 ++++ sci-biology/igv/igv-2.3.44.ebuild | 109 +++++++++++++------------------------- 2 files changed, 48 insertions(+), 71 deletions(-) diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog index 80d76fd..9eb94ff 100644 --- a/sci-biology/igv/ChangeLog +++ b/sci-biology/igv/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Mar 2015; Johann Schmitz <er...@gentoo.org> igv-2.3.44.ebuild: + Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as + requested by Martin Mokrejŝ (note: i've excluded the test code by passing + -Dnotests=true to ant so it may break at some point). Also improved the + ebuild by unbundling stuff we already have in portage. There are quite a + number of libraries which aren't used for compilation which may be needed at + runtime. I haven't tested the program in depth: it started at didn't throw + errors when i clicked around - everything else is way beyond my knowledge. + Improved the ebuild for sci-biology/igv + 17 Mar 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> igv-2.3.44.ebuild: fix inherit to use git instead of previously used subversion diff --git a/sci-biology/igv/igv-2.3.44.ebuild b/sci-biology/igv/igv-2.3.44.ebuild index f14d511..1464033 100644 --- a/sci-biology/igv/igv-2.3.44.ebuild +++ b/sci-biology/igv/igv-2.3.44.ebuild @@ -14,18 +14,13 @@ if [ "$PV" == "9999" ]; then EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git"; KEYWORDS="" else - SRC_URI="https://github.com/broadinstitute/IGV/archive/v"${PV}".zip"; + SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" KEYWORDS="" # binaries # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip fi -EANT_BUILD_TARGET="all" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_NEEDS_TOOLS="true" -WANT_ANT_TASKS="ant-apache-bcel" - DESCRIPTION="Integrative Genomics Viewer" HOMEPAGE="http://www.broadinstitute.org/igv/"; @@ -35,79 +30,51 @@ IUSE="" KEYWORDS="~amd64" COMMON_DEPS=" - dev-java/batik dev-java/absolutelayout - dev-java/jama - dev-java/commons-logging - dev-java/commons-math:3 - dev-java/concurrent-util - dev-java/jcommon - dev-java/jfreechart - dev-java/hdf-java - dev-java/jlfgr - dev-java/junit:0 - dev-java/log4j - dev-db/mysql-connector-c++ - sci-biology/samtools - dev-java/swing-layout - sci-biology/vcftools" -DEPEND=">=virtual/jdk-1.6:* + dev-java/jama:0 + dev-java/commons-logging:0 + >=dev-java/commons-io-2.1:1 + dev-java/commons-math:2 + dev-java/commons-jexl:2 + dev-java/jcommon:1.0 + dev-java/jfreechart:1.0 + dev-java/jlfgr:0 + dev-java/log4j:0 + dev-java/gson:2.2.2 + dev-java/guava:17 + dev-java/swing-layout:1 + dev-java/jgrapht:0 + dev-java/junit:4" + +DEPEND=">=virtual/jdk-1.7 + app-arch/unzip ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.6:* +RDEPEND=">=virtual/jre-1.7 ${COMMON_DEPS}" -S="${WORKDIR}"/IGV-"${PV}" +S="${WORKDIR}/IGV-${PV}" + +EANT_BUILD_TARGET="all" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_NEEDS_TOOLS="true" +EANT_EXTRA_ARGS="-Dnotests=true" + +EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," +EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4" + +java_prepare() { + mv lib oldlib || die + mkdir lib || die + + mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die + mv -v oldlib/batik* lib || die + + rm -rvf oldlib/* || die +} src_install() { java-pkg_newjar igv.jar - # probably could drop some of these below - # - # /usr/share/igv/lib/AbsoluteLayout.jar - # /usr/share/igv/lib/Jama-1.0.2.jar - # /usr/share/igv/lib/batik-awt-util.jar - # /usr/share/igv/lib/batik-bridge.jar - # /usr/share/igv/lib/batik-codec.jar - # /usr/share/igv/lib/batik-css.jar - # /usr/share/igv/lib/batik-dom.jar - # /usr/share/igv/lib/batik-ext.jar - # /usr/share/igv/lib/batik-gui-util.jar - # /usr/share/igv/lib/batik-gvt.jar - # /usr/share/igv/lib/batik-parser.jar - # /usr/share/igv/lib/batik-svg-dom.jar - # /usr/share/igv/lib/batik-svggen.jar - # /usr/share/igv/lib/batik-transcoder.jar - # /usr/share/igv/lib/batik-util.jar - # /usr/share/igv/lib/batik-xml.jar - # /usr/share/igv/lib/commons-logging-1.1.1.jar - # /usr/share/igv/lib/commons-math-1.1.jar - # /usr/share/igv/lib/concurrent.jar - # /usr/share/igv/lib/goby-io-igv.jar - # /usr/share/igv/lib/igv.jar - # /usr/share/igv/lib/jargs.jar - # /usr/share/igv/lib/jcommon-1.0.16.jar - # /usr/share/igv/lib/jfreechart-1.0.13.jar - # /usr/share/igv/lib/jhdf.jar - # /usr/share/igv/lib/jhdf5.jar - # /usr/share/igv/lib/jide-action.jar - # /usr/share/igv/lib/jide-common.jar - # /usr/share/igv/lib/jide-components.jar - # /usr/share/igv/lib/jide-dialogs.jar - # /usr/share/igv/lib/jide-dock.jar - # /usr/share/igv/lib/jide-grids.jar - # /usr/share/igv/lib/jlfgr-1_0.jar - # /usr/share/igv/lib/junit-4.5.jar - # /usr/share/igv/lib/log4j-1.2.15.jar - # /usr/share/igv/lib/mysql-connector-java-3.1.14-bin.jar - # /usr/share/igv/lib/sam-1.53.jar - # /usr/share/igv/lib/swing-layout-1.0.jar - # /usr/share/igv/lib/vcf.jar - # /usr/share/igv/lib/xml-apis-1.3.04.jar - # /usr/share/igv/lib/xml-apis-ext-1.3.04.jar - cd lib || die - rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar || die - cd .. || die - for i in lib/*.jar; do java-pkg_dojar $i; done java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main
