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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-ant-2 python-r1
# [ "$PV" == "9999" ] && inherit subversion
inherit subversion
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
if [ "$PV" == "9999" ]; then
ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
KEYWORDS=""
else
ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
KEYWORDS=""
fi
LICENSE="Tablet"
SLOT="0"
IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
>=virtual/jre-1.8:*"
# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
S="${WORKDIR}"
src_install() {
java-pkg_dojar lib/tablet.jar
java-pkg_dolauncher ${PN}
java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
java-pkg_dojar lib/picard*.jar
java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
doenvd 99Tablet
}
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