commit: c3ab7823c9462b681b308ab69346acc77cea683f Author: Johann Schmitz <ercpe <AT> gentoo <DOT> org> AuthorDate: Sun Apr 24 06:08:19 2016 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Sun Apr 24 06:10:23 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3ab7823
dev-java/htsjdk: New ebuild (dependency of picard-2) Package-Manager: portage-2.2.26 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 47 +++++++++++++++++++++++++++++++++++++ dev-java/htsjdk/metadata.xml | 15 ++++++++++++ 2 files changed, 62 insertions(+) diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild new file mode 100644 index 0000000..9950f1f --- /dev/null +++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="6" + +JAVA_PKG_IUSE="doc source" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats." +HOMEPAGE="https://samtools.github.io/htsjdk/"; +SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-java/commons-jexl:2 + dev-java/commons-compress:0 + dev-java/commons-logging:0" + +DEPEND=">=virtual/jdk-1.8 + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.8 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" + +java_prepare() { + rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die +} + +src_install() { + cd dist || die + + for i in *.jar; do + java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} + done + + use source && java-pkg_dosrc "${S}"/src/java/* + use doc && java-pkg_dojavadoc "${S}"/javadoc +} diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml new file mode 100644 index 0000000..513e863 --- /dev/null +++ b/dev-java/htsjdk/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Johann Schmitz (ercpe)</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">picard</remote-id> + </upstream> +</pkgmetadata>
