commit: da8f88f098f729e3f1d41ce540743453d31ab6e1 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Mar 11 19:35:54 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Mar 11 19:35:54 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=da8f88f0
version bump; vcftools-0.1.8-buildsystem.patch does not apply to current tree so using sed calls from within ebuild to mimic the tweaks Package-Manager: portage-2.2.15 sci-biology/vcftools/ChangeLog | 10 ++++++ sci-biology/vcftools/metadata.xml | 5 +++ sci-biology/vcftools/vcftools-0.1.12b.ebuild | 48 ++++++++++++++++++++++++++++ 3 files changed, 63 insertions(+) diff --git a/sci-biology/vcftools/ChangeLog b/sci-biology/vcftools/ChangeLog new file mode 100644 index 0000000..90e87e2 --- /dev/null +++ b/sci-biology/vcftools/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/vcftools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*vcftools-0.1.12b (11 Mar 2015) + + 11 Mar 2015; Martin Mokrejs <[email protected]> +metadata.xml, + +vcftools-0.1.12b.ebuild: + version bump; vcftools-0.1.8-buildsystem.patch does not apply to current tree + so using sed calls from within ebuild to mimic the tweaks diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/vcftools/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/vcftools/vcftools-0.1.12b.ebuild b/sci-biology/vcftools/vcftools-0.1.12b.ebuild new file mode 100644 index 0000000..bff0238 --- /dev/null +++ b/sci-biology/vcftools/vcftools-0.1.12b.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/vcftools/vcftools-0.1.8.ebuild,v 1.2 2013/02/27 16:39:18 jlec Exp $ + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P="${PN}_${PV}" + +DESCRIPTION="Tools for working with VCF (Variant Call Format) files" +HOMEPAGE="http://vcftools.sourceforge.net/"; +SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="lapack" + +RDEPEND="lapack? ( virtual/lapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + # epatch "${FILESDIR}"/${P}-buildsystem.patch # patch is outdated + sed -e 's#-O2#$(CXXFLAGS)#;s#-llapack#`$(PKG_CONFIG) --libs lapack`#' -i cpp/Makefile || die + tc-export CXX PKG_CONFIG +} + +src_compile() { + local myconf + use lapack && myconf="VCFTOOLS_PCA=1" + emake -C cpp ${myconf} +} + +src_install(){ + dobin cpp/${PN} + insinto /usr/share/${PN}/perl + doins perl/*.pm + exeinto /usr/share/${PN}/perl + doexe perl/{fill,vcf}-* + echo 'COLON_SEPARATED=PERL5LIB' > "${S}/99${PN}" + echo "PERL5LIB=/usr/share/${PN}/perl" >> "${S}/99${PN}" + doenvd "${S}/99${PN}" + dodoc README.txt +}
