commit: e09e5ec884dd0210694529c19b81fab9c48a76bc Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Sep 11 21:54:18 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Sep 11 21:54:18 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e09e5ec8
sci-biology/abyss: version bump An improved version with sealer using OpenMP+OpenMPI now. https://github.com/bcgsc/abyss/releases/tag/2.1.1 Package-Manager: Portage-2.3.48, Repoman-2.3.10 sci-biology/abyss/abyss-2.1.1.ebuild | 54 ++++++++++++++++++++++++++++++++++++ sci-biology/abyss/metadata.xml | 18 ++++++++++++ 2 files changed, 72 insertions(+) diff --git a/sci-biology/abyss/abyss-2.1.1.ebuild b/sci-biology/abyss/abyss-2.1.1.ebuild new file mode 100644 index 000000000..ccce937c7 --- /dev/null +++ b/sci-biology/abyss/abyss-2.1.1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +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 + )" + +# 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) +} diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml new file mode 100644 index 000000000..47116e507 --- /dev/null +++ b/sci-biology/abyss/metadata.xml @@ -0,0 +1,18 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>hask...@gentoo.org</email> + <name>Gentoo Haskell</name> + </maintainer> + <use> + <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> + </use> + <upstream> + <remote-id type="github">bcgsc/abyss</remote-id> + </upstream> +</pkgmetadata>
