commit: 9cb4024ef4caa9586b3ba4f1f73851a7dd449ddf Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 23:32:00 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 23:32:00 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9cb4024e
added some dev-java dependencies and removed some bundled .jar files Package-Manager: portage-2.2.7 --- sci-biology/igv/ChangeLog | 3 ++ sci-biology/igv/igv-2.0.35.ebuild | 66 ++++++++++++++++++++++++++++++++++++++- 2 files changed, 68 insertions(+), 1 deletion(-) diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog index de4a770..dec3275 100644 --- a/sci-biology/igv/ChangeLog +++ b/sci-biology/igv/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Mar 2014; Martin Mokrejs <[email protected]> igv-2.0.35.ebuild: + added some dev-java dependencies and removed some bundled .jar files + *igv-2.0.35 (23 Mar 2014) 23 Mar 2014; Martin Mokrejs <[email protected]> +igv-2.0.35.ebuild: diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild index 67a0c5b..457e8c8 100644 --- a/sci-biology/igv/igv-2.0.35.ebuild +++ b/sci-biology/igv/igv-2.0.35.ebuild @@ -22,7 +22,22 @@ SLOT="0" IUSE="" KEYWORDS="~amd64" -COMMON_DEPS="" +COMMON_DEPS="dev-java/batik + dev-java/absolutelayout + dev-java/jama + dev-java/commons-logging + dev-java/commons-math + dev-java/concurrent-util + dev-java/jcommon + dev-java/jfreechart + dev-java/hdf-java + dev-java/jlfgr + dev-java/junit + dev-java/log4j + dev-db/mysql-connector-c++ + sci-biology/samtools + dev-java/swing-layout + sci-biology/vcftools" DEPEND=">=virtual/jdk-1.6 ${COMMON_DEPS}" RDEPEND=">=virtual/jre-1.6 @@ -30,6 +45,55 @@ RDEPEND=">=virtual/jre-1.6 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 + cd .. + for i in lib/*.jar; do java-pkg_dojar $i; done + java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main }
