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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python2_7 )
inherit autotools flag-o-matic python-single-r1 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/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="
sci-biology/samtools:0.1-legacy
>=dev-libs/boost-1.62.0:=
${PYTHON_DEPS}"
DEPEND="
${RDEPEND}
dev-cpp/eigen:3
virtual/pkgconfig"
PATCHES=(
"${FILESDIR}"/${P}-samtools-legacy.patch
"${FILESDIR}"/${P}-flags.patch
"${FILESDIR}"/${P}-gcc6.patch
"${FILESDIR}"/${P}-boost-1.65-tr1-removal.patch
"${FILESDIR}"/${P}-gcc7.patch
"${FILESDIR}"/${P}-format-security.patch
"${FILESDIR}"/${P}-gcc5-make_shared.patch
)
src_prepare() {
default
python_fix_shebang src/cuffmerge
eautoreconf
}
src_configure() {
# keep in sync with Boost
append-cxxflags -std=c++14
append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
econf \
--disable-optim \
--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)/" \
--with-bam="${EPREFIX}/usr/" \
$(use_enable debug) \
PYTHON="${PYTHON}"
}
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