| # 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 |
| } |
