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

["Justin Lecher" <jlec@gentoo.org>]

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 <ercpe@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 <mmokrejs@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