commit: 57aaac2250383519cf73bc1d9d3fc20a1a3c8240 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Feb 24 13:57:44 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Feb 24 13:57:44 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57aaac22
sci-biology/verifyBamID: new package, would benefit unbundling of libStatGen Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/verifyBamID/metadata.xml | 12 ++++++++ sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild | 39 ++++++++++++++++++++++++ 2 files changed, 51 insertions(+) diff --git a/sci-biology/verifyBamID/metadata.xml b/sci-biology/verifyBamID/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/verifyBamID/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/verifyBamID/verifyBamID-1.1.3.ebuild b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild new file mode 100644 index 000000000..dfea2c485 --- /dev/null +++ b/sci-biology/verifyBamID/verifyBamID-1.1.3.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Verify sample identity/mix and genotype concordance" +HOMEPAGE="http://genome.sph.umich.edu/wiki/VerifyBamID"; +SRC_URI="https://github.com/statgen/verifyBamID/archive/v1.1.3.tar.gz -> ${P}.tar.gz + https://github.com/statgen/libStatGen/archive/v1.0.13.tar.gz -> libStatGen-1.0.13.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +# DEPEND="sci-libs/libStatGen" # TODO: currently it uses its own bundled copy +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + default + # unpack ./libStatGen-1.0.13/ contents + gzip -dc "${DISTDIR}"/libStatGen-1.0.13.tar.gz | tar xf - || die + ln -s libStatGen-1.0.13 libStatGen || die + cd "${WORKDIR}" || die + ln -s libStatGen-1.0.13 libStatGen || die +} + +src_compile(){ + # LIB_PATH_GENERAL="${EPREFIX}"/usr/"$(get_libdir)" emake + LIB_PATH_GENERAL="../libStatGen-1.0.13" emake +} + +src_install(){ + dobin bin/verifyBamID +}
