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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
MY_PV="3_0_1"
S="${WORKDIR}"/inGAP_"${MY_PV}"
inherit java-utils-2
DESCRIPTION="Detect SNPs and indels from Next-gen sequences using a Bayesian algorithm"
HOMEPAGE="
http://sites.google.com/site/nextgengenomics/ingap
http://sourceforge.net/projects/ingap/"
SRC_URI="http://sourceforge.net/projects/ingap/files/ingap/v"${PV}"/inGAP_"${MY_PV}".tgz"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
DEPEND=">=virtual/jre-1.7:*"
RDEPEND="${DEPEND}
dev-java/jfreechart
dev-java/swing-layout
dev-java/jcommon
dev-java/itext
dev-java/bytecode
sci-biology/biojava
dev-java/absolutelayout" # gnujaxp ?
src_install(){
java-pkg_dojar inGAP.jar
java-pkg_dolauncher inGAP --jar inGAP.jar
# dobin external/bin/{primer3_core, run_cpp, trf}
newdoc manual.pdf inGAP_Manual.pdf
dodoc doc/manual.htm
insinto /usr/share/inGAP/manual_files
doins doc/manual_files/*.png
}
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