commit: d3b79fddef20a7acf8d8cc6a49ca46830424065c Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Feb 19 17:53:40 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Feb 19 17:53:40 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d3b79fdd
sci-biology/lumpy-sv: new package, inventing installation layout https://github.com/arq5x/lumpy-sv/issues/168 Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/lumpy-sv/lumpy-sv-9999.ebuild | 39 +++++++++++++++++++++++++++++++ sci-biology/lumpy-sv/metadata.xml | 12 ++++++++++ 2 files changed, 51 insertions(+) diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild new file mode 100644 index 000000000..7c2fea620 --- /dev/null +++ b/sci-biology/lumpy-sv/lumpy-sv-9999.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 git-r3 + +DESCRIPTION="Probabilistic framework for structural variant discovery" +HOMEPAGE="https://github.com/arq5x/lumpy-sv"; +EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +# contains bundled htslib +DEPEND="dev-util/cmake" +RDEPEND="${DEPEND}" + +src_install(){ + cat > "${T}"/99lumpy-sv <<- EOF + LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv + PAIREND_DISTRO=${EPREFIX}/usr/share/lumpy-sv/scripts/pairend_distro.py + BAMGROUPREADS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py + BAMFILTERRG=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py + BAMLIBS=${EPREFIX}/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py + EOF + doenvd "${T}"/99lumpy-sv + rm -f bin/lumpyexpress.config + dobin bin/* + insinto /usr/share/lumpy-sv/scripts + for f in lumpy lumpy_filter lumpyexpress; do + rm bin/"$f" || die + done + doins scripts/* + dodoc README.md +} diff --git a/sci-biology/lumpy-sv/metadata.xml b/sci-biology/lumpy-sv/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/lumpy-sv/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>
