[gentoo-commits] gentoo-x86 commit in sci-biology/picard: picard-1.103.ebuild metadata.xml ChangeLog

[Johann Schmitz (ercpe)]

ercpe       13/11/24 15:21:14

  Modified:             metadata.xml ChangeLog
  Added:                picard-1.103.ebuild
  Log:
  Version bump and reworked ebuild for sci-biology/picard. Uses a snapshotted tarball from upstreams 1.103 subversion tag to meet gentoo qa requirements (wrt #491816)
  
  (Portage version: 2.2.7/cvs/Linux x86_64, signed Manifest commit with key 77C501ED)

Revision  Changes    Path
1.3                  sci-biology/picard/metadata.xml

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/metadata.xml?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/metadata.xml?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/metadata.xml?r1=1.2&r2=1.3

Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/picard/metadata.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- metadata.xml	11 Mar 2013 16:46:35 -0000	1.2
+++ metadata.xml	24 Nov 2013 15:21:14 -0000	1.3
@@ -1,5 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci-biology</herd>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>ercpe@g.o</email>
+		<name>Johann Schmitz (ercpe)</name>
+	</maintainer>
 </pkgmetadata>



1.4                  sci-biology/picard/ChangeLog

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/ChangeLog?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/ChangeLog?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/ChangeLog?r1=1.3&r2=1.4

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/picard/ChangeLog,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- ChangeLog	11 Mar 2013 16:46:35 -0000	1.3
+++ ChangeLog	24 Nov 2013 15:21:14 -0000	1.4
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/picard
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/ChangeLog,v 1.3 2013/03/11 16:46:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/ChangeLog,v 1.4 2013/11/24 15:21:14 ercpe Exp $
+
+*picard-1.103 (24 Nov 2013)
+
+  24 Nov 2013; Johann Schmitz <ercpe@g.o> +files/1.103-gentoo.patch,
+  +picard-1.103.ebuild, metadata.xml:
+  Version bump and reworked ebuild for sci-biology/picard. Uses a snapshotted
+  tarball from upstreams 1.103 subversion tag to meet gentoo qa requirements
+  (wrt #491816)
 
   11 Mar 2013; Justin Lecher <jlec@g.o> metadata.xml:
   Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
@@ -15,4 +23,3 @@
   04 Jan 2012; Andrey Kislyuk <weaver@g.o> +picard-1.58.ebuild,
   +metadata.xml:
   New package, ebuild written by me
-



1.1                  sci-biology/picard/picard-1.103.ebuild

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/picard-1.103.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/picard/picard-1.103.ebuild?rev=1.1&content-type=text/plain

Index: picard-1.103.ebuild
===================================================================
# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/picard/picard-1.103.ebuild,v 1.1 2013/11/24 15:21:14 ercpe Exp $

EAPI="5"

JAVA_PKG_IUSE="doc source test"
WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"

inherit java-pkg-2 java-ant-2

DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
HOMEPAGE="http://picard.sourceforge.net/"
SRC_URI="http://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"

LICENSE="Apache-2.0"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"

CDEPEND="dev-java/snappy:1.0
	dev-java/cofoja:0
	dev-java/commons-jexl:2
	dev-java/ant-core:0"

DEPEND=">=virtual/jdk-1.6
	dev-java/ant-apache-bcel:0
	test? (
		dev-java/testng:0
		dev-lang/R
	)
	${CDEPEND}"
RDEPEND=">=virtual/jre-1.6
	${CDEPEND}"

EANT_BUILD_TARGET="all"
EANT_TEST_TARGET="test"
EANT_NEEDS_TOOLS="true"
JAVA_ANT_REWRITE_CLASSPATH="true"
EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"

java_prepare() {
	mkdir "${S}"/lib || die

	epatch "${FILESDIR}"/${PV}-gentoo.patch

	mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
}

src_install() {
	cd dist || die

	for i in *-${PV}.jar; do
		java-pkg_newjar $i ${i/-${PV}/}
		rm $i || die
	done

	java-pkg_dojar *.jar
	for i in *.jar; do
		java-pkg_dolauncher ${i/.jar/} --jar $i;
	done

	use source && java-pkg_dosrc "${S}"/src/java/*
	use doc && java-pkg_dojavadoc "${S}"/javadoc
}

src_test() {
	java-pkg-2_src_test
}