[gentoo-commits] proj/sci:master commit in: sci-biology/igv/

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.cz> 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 <mmokrejs@×××××××××××××××.cz> +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
 }