sci-biology/jannovar: version bump, seems only one jar can be directly executed

https://github.com/charite/jannovar/issues/218
https://github.com/charite/jannovar/releases

Package-Manager: portage-2.3.2

1 files changed, 59 insertions, 0 deletions

diff --git a/sci-biology/jannovar/jannovar-0.17.ebuild b/sci-biology/jannovar/jannovar-0.17.ebuild
new file mode 100644
index 000000000..1e8ca0d0e
--- /dev/null
+++ b/sci-biology/jannovar/jannovar-0.17.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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
+}