commit: d8114ce881aac5e2972066606955071fa0ae4fde Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jul 12 16:04:10 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jul 12 16:04:10 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8114ce8
sci-biology/cramtools: new package, not working yet will not compile with java8 until upstream issue #59 is fixed contains bundled dev-java/htsjdk (although other apps do not keep up with the API changes in htsjdk so it does have a reason) Package-Manager: portage-2.2.28 sci-biology/cramtools/cramtools-3.0.ebuild | 32 ++++++++++++++++++++++++++++++ sci-biology/cramtools/metadata.xml | 12 +++++++++++ 2 files changed, 44 insertions(+) diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild new file mode 100644 index 0000000..9d903a2 --- /dev/null +++ b/sci-biology/cramtools/cramtools-3.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java tools and APIs for efficient compression of sequence read data" +HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit + https://github.com/enasequence/cramtools"; +SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + >=virtual/jdk-1.7:* + dev-java/ant-core + dev-java/htsjdk" +RDEPEND=" + ${DEPEND} + >=virtual/jre-1.7:*" + +# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk? +# https://github.com/enasequence/cramtools/issues/58 +# https://github.com/enasequence/cramtools/issues/59 +src_compile(){ + ant -f build/build.xml runnable || die +} diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/cramtools/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>
