commit: 6c252245a4ab18f5d211723f9078682dfa06bd00 Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com> AuthorDate: Thu Apr 22 07:23:16 2021 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Apr 22 07:23:16 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c252245
sci-biology/abyss: add 2.3.1 release but keep patches The PathConsensus crash fixes were not included by upstream, keep them. Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com> sci-biology/abyss/abyss-2.3.1.ebuild | 58 ++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild b/sci-biology/abyss/abyss-2.3.1.ebuild new file mode 100644 index 000000000..d9134813b --- /dev/null +++ b/sci-biology/abyss/abyss-2.3.1.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +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 -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="+mpi openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost:= + misc-haskell? ( + dev-libs/gmp:0= + dev-libs/libffi:0= + ) + mpi? ( sys-cluster/openmpi )" +DEPEND="${RDEPEND} + misc-haskell? ( + dev-lang/ghc + )" + +PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch + "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch + ) + +# 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) --enable-maxk=256 +}
