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+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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"
+
+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=(
+	"${FILESDIR}/${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)
+}