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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-19 18:53:40 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-19 18:53:40 +0100 |
| commit | d3b79fddef20a7acf8d8cc6a49ca46830424065c (patch) | |
| tree | 6ad687ca5e8b45e28ef95e7112b8940ad0b00378 /sci-biology/lumpy-sv | |
| parent | Merge branch 'master' of git+ssh://git.gentoo.org/proj/sci (diff) | |
| download | sci-d3b79fddef20a7acf8d8cc6a49ca46830424065c.tar.gz sci-d3b79fddef20a7acf8d8cc6a49ca46830424065c.tar.bz2 sci-d3b79fddef20a7acf8d8cc6a49ca46830424065c.zip | |
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
Diffstat (limited to 'sci-biology/lumpy-sv')
| -rw-r--r-- | sci-biology/lumpy-sv/lumpy-sv-9999.ebuild | 39 | ||||
| -rw-r--r-- | sci-biology/lumpy-sv/metadata.xml | 12 |
2 files changed, 51 insertions, 0 deletions
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>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> |