From ea24d150f34cadee6954bc5f70e808a1fdb27375 Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Thu, 5 Jan 2012 23:00:11 +0000 Subject: [PATCH] Version bump Package-Manager: portage-2.2.0_alpha74/cvs/Linux x86_64 --- sci-biology/goby-cpp/ChangeLog | 9 +++- sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild | 26 +++++++++ sci-biology/goby/ChangeLog | 9 +++- sci-biology/goby/goby-1.9.8.1.ebuild | 57 ++++++++++++++++++++ 4 files changed, 97 insertions(+), 4 deletions(-) create mode 100644 sci-biology/goby-cpp/goby-cpp-1.9.8.1.ebuild create mode 100644 sci-biology/goby/goby-1.9.8.1.ebuild diff --git a/sci-biology/goby-cpp/ChangeLog b/sci-biology/goby-cpp/ChangeLog index bec00b1eede4..569c41d48c00 100644 --- 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 +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 index 000000000000..90247aae1f8b --- /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 217521d6dc03..74a65c041ef5 100644 --- 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 +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 index 000000000000..34b5acfc6a6c --- /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 +} -- 2.26.2