commit: 62afc0eb5df8a6b490373a37d801ff4e7d373613 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Feb 11 20:47:13 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Feb 11 20:47:13 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=62afc0eb
sci-biology/grass: new package, see bugs at github.com Package-Manager: portage-2.2.26 sci-biology/grass/grass-20130628.ebuild | 39 +++++++++++++++++++++++++++++++++ sci-biology/grass/metadata.xml | 12 ++++++++++ 2 files changed, 51 insertions(+) diff --git a/sci-biology/grass/grass-20130628.ebuild b/sci-biology/grass/grass-20130628.ebuild new file mode 100644 index 0000000..9744012 --- /dev/null +++ b/sci-biology/grass/grass-20130628.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Scaffold next-generation sequencing assemblies" +HOMEPAGE="https://github.com/AlexeyG/GRASS"; +SRC_URI="https://github.com/AlexeyG/GRASS/archive/master.zip -> grass-20130628.zip + https://tud-scaffolding.googlecode.com/files/GRASS%20manual.pdf -> grass_manual.pdf" +# EGIT_REPO_URI="https://github.com/AlexeyG/GRASS.git"; + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# some IBM development CPLEX library? +# ilcplex/ilocplex.h: No such file or directory +DEPEND="sci-biology/bamtools + sci-biology/ncbi-tools++" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/GRASS-master + +src_prepare(){ + sed -e 's#/data/bio/alexeygritsenk/apps/include/ncbi-tools++#/usr/include/ncbi-tools++#' -i Makefile.config || die + sed -e 's#/data/bio/alexeygritsenk/apps/include/#/usr/include/bamtools#' -i Makefile.config || die + sed -e 's#/data/bio/alexeygritsenk/apps/lib#/usr/lib64#' -i Makefile.config || die +} + +src_compile(){ + emake all +} + +src_install(){ + dodoc "${DISTDIR}"/grass_manual.pdf manual/manual.tex + dobin bin/* +} diff --git a/sci-biology/grass/metadata.xml b/sci-biology/grass/metadata.xml new file mode 100644 index 0000000..1699e58 --- /dev/null +++ b/sci-biology/grass/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>
