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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
inherit java-pkg-2 java-ant-2
DESCRIPTION="Manipulate and analyze VCF files"
HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"
SRC_URI="https://github.com/RealTimeGenomics/rtg-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-2"
SLOT="0"
KEYWORDS="~amd64"
DEPEND="
>=virtual/jdk-1.8:*
>=dev-java/ant-core-1.9
dev-java/jython"
RDEPEND="${DEPEND}
>=virtual/jre-1.8:*"
src_compile(){
ant zip-nojre || die
}
# "${S}"/lib/sam-2.9.1.jar
# "${S}"/lib/findbugs-annotations.jar
# "${S}"/lib/findbugs-jsr305.jar
# "${S}"/lib/velocity-tools-generic.jar
# "${S}"/lib/RPlot.jar
# "${S}"/lib/commons-collections-3.2.1.jar
# "${S}"/lib/velocity-1.7.jar
# "${S}"/lib/commons-compress-1.4.1.jar
# "${S}"/lib/commons-lang-2.4.jar
# "${S}"/lib/jumble-annotations.jar
# "${S}"/lib/sam-2.9.1-src.jar
# "${S}"/lib/gzipfix.jar
# "${S}"/buildLib/ant-contrib-1.0b3.jar
# "${S}"/buildLib/handlechecker.jar
# "${S}"/testLib/hamcrest-core-1.3.jar
# "${S}"/testLib/junit.jar
# "${S}"/testLib/spelling.jar
src_install(){
dobin installer/rtg
insinto /usr/share/"${PN}"
doins build/rtg-tools.jar
doins lib/gzipfix.jar
dodoc installer/resources/tools/RTGOperationsManual.pdf
doins -r installer/resources/tools/RTGOperationsManual
dodoc installer/resources/tools/scripts/README.txt
dodoc installer/ReleaseNotes.txt
# TODO
# extract more files from the generated rtg-tools-3.11-39691f9f-base.zip
# file or better the installer/resources/ source directory
#
# install installer/resources/common/scripts/rtg-bash-completion
}
src_test(){
ant runalltests || die
}
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