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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit java-pkg-2 java-ant-2
DESCRIPTION="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor"
HOMEPAGE="http://www.broadinstitute.org/annotation/conrad
http://sourceforge.net/projects/conradcrf"
SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"
LICENSE="LGPL-2.1"
SLOT="0"
KEYWORDS=""
IUSE=""
# upstream binaries do not work with oracle-java-8
RDEPEND="
>=virtual/jre-1.5:*
<=virtual/jre-1.7:*
dev-java/commons-logging
>=dev-java/commons-lang-2.1:*
dev-java/colt
dev-java/dom4j
"
# spring # see bug #97004
# dev-java/LBFGS # LBFGS is a numericla library we use internally for the solver
DEPEND="${RDEPEND}
>=virtual/jdk-1.5:*
<=virtual/jdk-1.7:*
dev-java/ant-core
>=dev-java/jfreechart-1.0.3
>=dev-java/jcommon-1.0.6
>=dev-java/commons-math-1.1
"
S="${WORKDIR}"
src_prepare(){
sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
}
src_compile(){
cd dev || die
ant compile || die
}
src_install() {
dobin bin/conrad.sh
java-pkg_newjar lib/conrad.jar
java-pkg_dojar lib/conrad.jar
java-pkg_dolauncher conrad --jar conrad.jar
insinto /usr/share/conrad
dodoc -r docs models samples trainingFiles
}
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