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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit autotools
DESCRIPTION="Algorithm for detecting SNPs, indels, and other polymorphisms"
HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd/"
SRC_URI="
ftp://ftp.broad.mit.edu/pub/crd/VAAL/latest_source_code/${P}.tar.gz
ftp://ftp.broad.mit.edu/pub/crd/VAAL/VAAL_manual.doc
https://dev.gentoo.org/~mgorny/dist/${P}_remove-namespace-std.patch.bz2"
LICENSE="Whitehead-MIT"
SLOT="0"
KEYWORDS="amd64"
IUSE="openmp"
RDEPEND="
!sci-biology/allpaths
!sci-biology/allpathslg"
DEPEND="
${RDEPEND}
dev-libs/boost"
DOCS=( "${DISTDIR}/VAAL_manual.doc" )
PATCHES=(
"${WORKDIR}/${P}_remove-namespace-std.patch"
)
src_prepare() {
sed \
-e '/COPYING/d' \
-i src/Makefile.am || die
sed \
-e 's:-ggdb::g' \
-e '/AC_OPENMP_CEHCK/d' \
-i configure.ac || die
default
eautoreconf
}
src_configure() {
econf \
$(use_enable openmp)
}
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