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# 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
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