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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 toolchain-funcs
DESCRIPTION="Transcript assembly, differential expression, and differential regulation for RNA-Seq"
HOMEPAGE="http://cufflinks.cbcb.umd.edu/"
SRC_URI="http://cufflinks.cbcb.umd.edu/downloads/${P}.tar.gz"
SLOT="0"
LICENSE="Artistic"
IUSE="debug"
KEYWORDS="~amd64 ~x86"
DEPEND="
|| (
(
>=sci-biology/samtools-0.1.18
sci-libs/htslib
)
<sci-biology/samtools-1
)
>=dev-libs/boost-1.47.0:=
<dev-libs/boost-1.56.0:=
dev-cpp/eigen:3
"
RDEPEND="${DEPEND}"
PATCHES=(
"${FILESDIR}"/${P}-hts.patch
"${FILESDIR}"/${P}-flags.patch
)
src_prepare() {
append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
autotools-utils_src_prepare
}
src_configure() {
local myeconfargs=(
--disable-optim
--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/"
--with-bam="${EPREFIX}/usr/"
$(use_enable debug)
)
autotools-utils_src_configure
}
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