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authorSergei Trofimovich <slyfox@gentoo.org>2020-06-21 17:46:53 +0100
committerSergei Trofimovich <slyfox@gentoo.org>2020-06-21 17:47:16 +0100
commit4499edbc478106c4f7a04062c8ee2f273474c8cb (patch)
treea875ad7e0ef0ed58d9dc0276355147107c6d9f0f /sci-biology/abyss/abyss-2.0.3-r1.ebuild
parentsci-libs/proj: Drop 7.0.0 (diff)
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sci-biology/abyss: switch from virtual/libffi
Package-Manager: Portage-2.3.101, Repoman-2.3.22 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org>
Diffstat (limited to 'sci-biology/abyss/abyss-2.0.3-r1.ebuild')
-rw-r--r--sci-biology/abyss/abyss-2.0.3-r1.ebuild64
1 files changed, 0 insertions, 64 deletions
diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
deleted file mode 100644
index 800a45964cd..00000000000
--- a/sci-biology/abyss/abyss-2.0.3-r1.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# 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
- )"
-
-PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
-
-# GHC uses it's own native code generator. Portage's
-# QA check generates false positive because it assumes
-# presence of GCC-specific sections.
-#
-# Workaround false positiove by disabling the check completely.
-# bug #677600
-QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak'
-
-# 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)
-}