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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
DESCRIPTION="Exome annotation tool"
HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html"
SRC_URI="https://github.com/charite/jannovar/archive/v"${PV}".tar.gz -> ${P}.tar.gz"
# https://github.com/charite/jannovar
LICENSE="BSD-2"
SLOT="0"
KEYWORDS=""
IUSE=""
COMMON_DEPS="
dev-java/commons-compress
dev-java/commons-io
dev-java/commons-jexl:*
dev-java/commons-logging:0
dev-java/commons-net
dev-java/guava:*
dev-java/hamcrest-core:*
dev-java/htsjdk
dev-java/ini4j
dev-java/junit:*
dev-java/log4j:0"
DEPEND=">=virtual/jdk-1.6
dev-java/maven-bin:*
${COMMON_DEPS}"
RDEPEND=">=virtual/jre-1.6
${COMMON_DEPS}"
# TODO: set a proxy because it downloads data during compile step
# http://jannovar.readthedocs.io/en/master/install.html
# see https://github.com/charite/jannovar/issues/218
# https://maven.apache.org/settings.html#Proxies
src_compile(){
mvn package -Dmaven.test.skip.exec=true -DskipTests=true -Duser.home="${HOME}" || die
}
src_install(){
# maven download 95MB from the network into "${PORTAGE_BUILDDIR}/homedir/"
export M2="${HOME}"
mvn install -Dmaven.test.skip.exec=true -Duser.home="${HOME}" || die
# jannovar-cli-${PV}.jar includes all libraries (jannovar and others like htsjdk)
java-pkg_dojar jannovar-cli/target/jannovar-cli-"${PV}".jar
java-pkg_dolauncher jannovar-cli --jar jannovar-cli-"${PV}".jar
# original-jannovar-cli-0.17.jar contains only the source files of the specific package
java-pkg_dojar jannovar-cli/target/original-jannovar-cli-"${PV}".jar
java-pkg_dojar jannovar-hgvs/target/jannovar-hgvs-"${PV}".jar
java-pkg_dojar jannovar-htsjdk/target/jannovar-htsjdk-"${PV}".jar
java-pkg_dojar jannovar-core/target/jannovar-core-"${PV}".jar
java-pkg_dojar jannovar-vardbs/target/jannovar-vardbs-"${PV}".jar
java-pkg_dojar jannovar-inheritance-checker/target/jannovar-inheritance-checker-"${PV}".jar
}
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