commit: 42bcef7f16f3999182b38951f69ce0e15d1ef58a Author: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org> AuthorDate: Thu Mar 15 23:30:40 2018 +0000 Commit: Sergei Trofimovich <slyfox <AT> gentoo <DOT> org> CommitDate: Thu Mar 15 23:33:14 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=42bcef7f
sci-biology/abyss: bump up to 2.0.3 Package-Manager: Portage-2.3.24, Repoman-2.3.6 sci-biology/abyss/Manifest | 1 + sci-biology/abyss/abyss-2.0.3.ebuild | 54 ++++++++++++++++++++++++++++++++++++ 2 files changed, 55 insertions(+) diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index 20d851c721d..b18ccd65238 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1 +1,2 @@ DIST abyss-2.0.2.tar.gz 1036135 BLAKE2B 6781a63203b5e6a1de70837a6dad7c79643d049b4c1e4b827471f2414cc821f82d98f9856518e3c24486e068c584520d0a1852d4e03d26247b896c776baaee41 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 +DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 diff --git a/sci-biology/abyss/abyss-2.0.3.ebuild b/sci-biology/abyss/abyss-2.0.3.ebuild new file mode 100644 index 00000000000..ccce937c77c --- /dev/null +++ b/sci-biology/abyss/abyss-2.0.3.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) +}
