commit: 9ce6536356df2dffa9672161ae47b8de609c7682 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jul 12 16:28:58 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jul 12 16:28:58 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ce65363
dev-java/htsjdk: re-added back 2.2.2 version due to picard-2 Package-Manager: portage-2.2.28 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 48 +++++++++++++++++++++++++++++++++++++ 1 file changed, 48 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..ca2cdd9 --- /dev/null +++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild @@ -0,0 +1,48 @@ +# 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() { + default + 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 +}
