commit: a58f8020918ebfc342dd2c596e4c25441bd665db Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Aug 26 08:40:58 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Aug 26 08:40:58 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a58f8020
sci-biology/vcflib: new package, works though is not ideal Package-Manager: portage-2.3.0 sci-biology/vcflib/metadata.xml | 12 ++++++++++ sci-biology/vcflib/vcflib-9999.ebuild | 43 +++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+) diff --git a/sci-biology/vcflib/metadata.xml b/sci-biology/vcflib/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/vcflib/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>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/vcflib/vcflib-9999.ebuild b/sci-biology/vcflib/vcflib-9999.ebuild new file mode 100644 index 0000000..5a03fe4 --- /dev/null +++ b/sci-biology/vcflib/vcflib-9999.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 toolchain-funcs + +DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)" +HOMEPAGE="https://github.com/vcflib/vcflib"; +EGIT_REPO_URI="https://github.com/vcflib/vcflib.git"; + +# vcflib is incorporated into several projects, such as freebayes + +LICENSE="MIT-with-advertising" +SLOT="0" +KEYWORDS="" +IUSE="mpi" + +DEPEND="mpi? ( sys-cluster/openmpi )" +RDEPEND="${DEPEND}" +# contains bundled sci-biology/htslib ? +# see also ./include for possible traces of other bundled sw + +src_prepare(){ + default + sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/" -i Makefile || die + sed -e "s/^CXXFLAGS = -O3/CXXFLAGS = ${CXXFLAGS}/" -i Makefile || die +} + +src_compile(){ + if use mpi ; then + emake openmp + else + emake + fi +} + +src_install(){ + dobin bin/* + dolib lib/* # install libvcflib.a + dodoc README.md +}
