# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2

EAPI=6

inherit autotools flag-o-matic toolchain-funcs

DESCRIPTION="Transcript assembly and differential expression/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-legacy
	>=dev-libs/boost-1.59.0:=
	dev-cpp/eigen:3"
RDEPEND="${DEPEND}"

PATCHES=(
	"${FILESDIR}"/${P}-samtools-legacy.patch
	"${FILESDIR}"/${P}-flags.patch
	"${FILESDIR}"/${P}-gcc6.patch
)

src_prepare() {
	default
	eautoreconf
	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
}

src_configure() {
	econf --disable-optim \
		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
		--with-bam="${EPREFIX}/usr/" \
		$(use_enable debug)
}