diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/abyss/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/abyss/abyss-2.3.4.ebuild | 57 |
2 files changed, 58 insertions, 0 deletions
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest index e03409dd93f2..32cead3a3a6e 100644 --- a/sci-biology/abyss/Manifest +++ b/sci-biology/abyss/Manifest @@ -1 +1,2 @@ DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570 +DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4 diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild new file mode 100644 index 000000000000..c2e1ffd29b32 --- /dev/null +++ b/sci-biology/abyss/abyss-2.3.4.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/" +SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="openmp misc-haskell" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-cpp/sparsehash + dev-libs/boost:= + misc-haskell? ( + dev-libs/gmp:0= + dev-libs/libffi:0= + ) + sys-cluster/openmpi + dev-db/sqlite:3 +" +DEPEND="${RDEPEND} + misc-haskell? ( + dev-lang/ghc + ) +" + +# todo: --enable-maxk=N configure option +# todo: also allow build with mpich (--enable-mpich) + +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 +} |