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| author |   Martin Mokrejš <mmokrejs@gmail.com> | 2017-01-10 14:32:37 +0100 |
|---|---|---|
| committer |   David Seifert <soap@gentoo.org> | 2017-01-15 18:53:17 +0100 |
| commit | 6764ffe099c90b89117afeb0087258ec76f3136f (patch) | |
| tree | 9945e7170da61c9bf3360c8fa68902eabcb89c3d /sci-biology/abyss/abyss-2.0.2-r1.ebuild | |
| parent | app-admin/salt: random_org unittest was moved to integration tests (diff) | |
| download | gentoo-6764ffe099c90b89117afeb0087258ec76f3136f.tar.gz gentoo-6764ffe099c90b89117afeb0087258ec76f3136f.tar.bz2 gentoo-6764ffe099c90b89117afeb0087258ec76f3136f.zip | |
sci-biology/abyss: only openmpi is supported
Closes: https://github.com/gentoo/gentoo/pull/3414
Diffstat (limited to 'sci-biology/abyss/abyss-2.0.2-r1.ebuild')
| -rw-r--r-- | sci-biology/abyss/abyss-2.0.2-r1.ebuild | 56 |
1 files changed, 56 insertions, 0 deletions
diff --git a/sci-biology/abyss/abyss-2.0.2-r1.ebuild b/sci-biology/abyss/abyss-2.0.2-r1.ebuild new file mode 100644 index 000000000000..4533f9b824d6 --- /dev/null +++ b/sci-biology/abyss/abyss-2.0.2-r1.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit autotools 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="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost:= + misc-haskell? ( + dev-libs/gmp:0= + virtual/libffi:0= + ) + mpi? ( sys-cluster/openmpi )" +DEPEND="${RDEPEND} + misc-haskell? ( + dev-lang/ghc + dev-haskell/mmap + )" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +src_prepare() { + default + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + # disable building haskell tool Misc/samtobreak + # unless request by user: bug #534412 + use misc-haskell || export ac_cv_prog_ac_ct_GHC= + + econf $(use_enable openmp) +} |