Version bump

Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64

diff --git a/sci-biology/goby-cpp/ChangeLog b/sci-biology/goby-cpp/ChangeLog
index bec00b1eede4db28cd34d11124427d03ff6f3407..569c41d48c006c66a1535adabff5d9df730befb9 100644 (file)
--- a/sci-biology/goby-cpp/ChangeLog
+++ b/sci-biology/goby-cpp/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/goby-cpp
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby-cpp/ChangeLog,v 1.1 2011/09/25 21:45:36 weaver Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby-cpp/ChangeLog,v 1.2 2012/01/05 22:58:47 weaver Exp $
+
+*goby-cpp-1.9.8.1 (05 Jan 2012)
+
+  05 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +goby-cpp-1.9.8.1.ebuild:
+  Version bump
 
 *goby-cpp-1.9.7.3 (25 Sep 2011)
 

diff --git a/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild
new file mode 100644 (file)
index 0000000..90247aa
--- /dev/null
+++ b/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild,v 1.1 2012/01/05 22:58:47 weaver Exp $
+
+EAPI=4
+
+inherit autotools
+
+DESCRIPTION="A DNA sequencing data management framework - C/C++ API"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-goby_${PV}/goby_${PV}-cpp.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=">=dev-libs/protobuf-2.4.1
+       >=dev-libs/libpcre-8.12"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/goby_${PV}/cpp"
+
+src_prepare() {
+       eautoreconf
+}

diff --git a/sci-biology/goby/ChangeLog b/sci-biology/goby/ChangeLog
index 217521d6dc03b2b9a89bbe56ba97917cb1137422..74a65c041ef5e498d4557a8578edcda1c1658c0a 100644 (file)
--- a/sci-biology/goby/ChangeLog
+++ b/sci-biology/goby/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/goby
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/ChangeLog,v 1.1 2011/09/25 21:50:28 weaver Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/ChangeLog,v 1.2 2012/01/05 23:00:11 weaver Exp $
+
+*goby-1.9.8.1 (05 Jan 2012)
+
+  05 Jan 2012; Andrey Kislyuk <weaver@gentoo.org> +goby-1.9.8.1.ebuild:
+  Version bump
 
 *goby-1.9.7.3 (25 Sep 2011)
 

diff --git a/sci-biology/goby/goby-1.9.8.1.ebuild b/sci-biology/goby/goby-1.9.8.1.ebuild
new file mode 100644 (file)
index 0000000..34b5acf
--- /dev/null
+++ b/sci-biology/goby/goby-1.9.8.1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/goby/goby-1.9.8.1.ebuild,v 1.1 2012/01/05 23:00:11 weaver Exp $
+
+EAPI=4
+
+ESVN_REPO_URI="https://pbtech-vc.med.cornell.edu/public/svn/icb/trunk/goby"
+EANT_GENTOO_CLASSPATH="commons-logging,commons-lang-2.1,commons-io-1,protobuf,fastutil-5.0,log4j,jsap,commons-configuration,commons-math-2"
+EANT_GENTOO_CLASSPATH_EXTRA="lib/icb-utils.jar:lib/edu.mssm.crover.cli.jar:lib/JRI.jar:lib/dsiutils-1.0.12.jar"
+
+JAVA_ANT_REWRITE_CLASSPATH="true"
+
+#inherit java-pkg-2 java-ant-2 subversion
+inherit java-pkg-2 java-ant-2
+
+MY_P="${PN}_${PV}"
+
+DESCRIPTION="A DNA sequencing data management framework"
+HOMEPAGE="http://campagnelab.org/software/goby/"
+SRC_URI="http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-src.zip
+       http://chagall.med.cornell.edu/goby/releases/archive/release-${MY_P}/${MY_P}-deps.zip"
+
+LICENSE="GPL-3 LGPL-3"
+SLOT="0"
+IUSE="+cpp"
+KEYWORDS="~amd64 ~x86"
+
+COMMON_DEPS="dev-java/commons-logging
+       dev-java/commons-lang:2.1
+       dev-java/commons-io:1
+       dev-libs/protobuf[java]
+       dev-java/fastutil:5.0
+       dev-java/log4j
+       dev-java/jsap
+       dev-java/commons-configuration
+       dev-java/commons-math:2"
+DEPEND=">=virtual/jdk-1.6
+       ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+       ${COMMON_DEPS}
+       cpp? ( ~sci-biology/goby-cpp-${PV} )"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+       sed -i '/sge/ d' build.xml || die
+       java-pkg-2_src_prepare
+}
+
+src_install() {
+       java-pkg_dojar goby*.jar
+       java-pkg_dolauncher goby --jar goby.jar
+
+       insinto /usr/share/${PN}
+       doins -r python
+       dodoc CHANGES.txt
+}