From 4c3880bfe25f6b81461523e3f1f38b43614d51b9 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Sat, 23 May 2015 23:51:58 +0200 Subject: sci-biology/amos: bring in upstream patch to cope with secondary alignments from 'bwa mem -M' Package-Manager: portage-2.2.18 --- sci-biology/abyss/abyss-1.3.3-r1.ebuild | 42 +++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 sci-biology/abyss/abyss-1.3.3-r1.ebuild (limited to 'sci-biology/abyss/abyss-1.3.3-r1.ebuild') diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild new file mode 100644 index 000000000..b7278619c --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.3-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.5 2013/08/11 14:55:22 jlec Exp $ + +EAPI="4" + +inherit autotools eutils toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +src_prepare() { + tc-export AR + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-ac_prog_ar.patch \ + "${FILESDIR}"/${P}-samtoafg.patch + + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + econf \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable openmp) +} -- cgit v1.2.3-65-gdbad