commit: 3372b8cbc1e81f2e39d8bc5247ee9176abfe90bb Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jun 23 15:26:06 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jun 23 15:26:06 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3372b8cb
sci-biology/jannovar: first attempt at a new package Package-Manager: portage-2.2.28 sci-biology/jannovar/jannovar-0.16.ebuild | 35 +++++++++++++++++++++++++++++++ sci-biology/jannovar/metadata.xml | 12 +++++++++++ 2 files changed, 47 insertions(+) diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild b/sci-biology/jannovar/jannovar-0.16.ebuild new file mode 100644 index 0000000..9dcbd17 --- /dev/null +++ b/sci-biology/jannovar/jannovar-0.16.ebuild @@ -0,0 +1,35 @@ +# 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/v0.16.tar.gz -> ${P}.tar.gz" + +# https://github.com/charite/jannovar +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=virtual/jdk-1.6 + dev-java/maven-bin:*" +RDEPEND=">=virtual/jre-1.6" + +# 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 +src_compile(){ + mvn package -Dmaven.test.skip.exec=true -DskipTests=true || die +} + +src_install(){ + mvn install -Dmaven.test.skip.exec=true || die + dojar *.jar + java-pkg_newjar jannovar-bin.jar + java-pkg_dolauncher jannovar-bin --jar jannovar-bin.jar +} diff --git a/sci-biology/jannovar/metadata.xml b/sci-biology/jannovar/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/jannovar/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata>
