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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
AUTOTOOLS_AUTORECONF=true
inherit autotools-utils flag-o-matic
DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
# see also http://www.broadinstitute.org/software/allpaths-lg/blog/?page_id=12
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64"
IUSE="openmp"
DEPEND="
dev-libs/boost
!sci-biology/allpaths
sci-biology/vaal"
RDEPEND=""
pkg_pretend() {
# as of release 44849, GCC 4.7.0 (or higher) is required
# seems pre gcc-4.7 users must stay with:
# ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-01/allpathslg-44837.tar.gz
if [[ ${MERGE_TYPE} != binary ]]; then
[[ $(tc-getCC) == *gcc* ]] && [[ $(gcc-version) < 4.7 ]] && \
die "You need to use gcc >4.7"
fi
}
src_prepare() {
local i
sed \
-e 's/-ggdb//' \
-e 's:CEHCK:CHECK:g' \
-i configure.ac || die
for i in QueryLookupTable ScaffoldAccuracy MakeLookupTable Fastb ShortQueryLookup; do
sed -e "/bin_PROGRAMS/s: ${i} : :g" -i src/Makefile.am || die
done
autotools-utils_src_prepare
}
src_configure() {
local myeconfargs=(
$(use_enable openmp)
)
autotools-utils_src_configure
}
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