commit: 0dc9a5177e72dac73b0ce8e8de20925b5e6df227 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Feb 10 17:05:29 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Feb 10 17:05:29 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0dc9a517
sci-biology/cg-cat: new package Package-Manager: portage-2.2.26 sci-biology/cg-cat/cg-cat-20150130.ebuild | 43 +++++++++++++++++++++++++++++++ sci-biology/cg-cat/metadata.xml | 12 +++++++++ 2 files changed, 55 insertions(+) diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild new file mode 100644 index 0000000..39444ec --- /dev/null +++ b/sci-biology/cg-cat/cg-cat-20150130.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="r2cat and treecat, scaffolding tools for ordering and orienting contigs" +HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/cgcat"; +SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.tar.gz"; +# SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.jar"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=virtual/jre-1.6:*" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/r2cat + +src_prepare(){ + sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile +} + +src_compile(){ + emake +} + +src_install(){ + # emake install dies with: + # jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat cg-cat.jar cgcat + # Enter Passphrase for keystore: jarsigner: you must enter key password + # Makefile:44: recipe for target 'cg-cat.jar' failed + mkdir -p "${D}"/usr/share/r2cat + emake install_cebitec + emake install_bibiserv +} + +# java -Xmx1024M -jar r2cat.jar +# java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64 diff --git a/sci-biology/cg-cat/metadata.xml b/sci-biology/cg-cat/metadata.xml new file mode 100644 index 0000000..1699e58 --- /dev/null +++ b/sci-biology/cg-cat/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +<maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
