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Diffstat (limited to 'sci-biology/abyss/abyss-1.9.0.ebuild')
-rw-r--r--sci-biology/abyss/abyss-1.9.0.ebuild53
1 files changed, 53 insertions, 0 deletions
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild
new file mode 100644
index 00000000000..c32b477ad42
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.9.0.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/1.9.0.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost
+ misc-haskell? ( dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}
+ misc-haskell? ( dev-lang/ghc
+ dev-haskell/mmap )
+"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-ac_prog_ar.patch
+ "${FILESDIR}"/${P}-gcc-6.patch
+)
+
+src_prepare() {
+ default
+ tc-export AR
+ 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)
+}