cufflinks-1.3.0.ebuild

cufflinks-2.1.1.ebuild (text/plain), 1.45 KB, created by Mahn on 2013-12-23 10:13:02 UTC

# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/cufflinks/cufflinks-2.1.1.ebuild,v 1.3 2013/12/20 10:58:55 mahn Exp $
# based on jlec ebuild

EAPI=4

AUTOTOOLS_AUTORECONF=yes

inherit autotools-utils

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
        dev-libs/boost[threads]
        dev-cpp/eigen"

RDEPEND="${DEPEND}"

#PATCHES=(
#       "${FILESDIR}"/${P}-autotools.patch
#       "${FILESDIR}"/${P}-boost.patch
#       "${FILESDIR}"/${P}-gcc-4.7.patch
#       )

src_prepare() {
        # The include dir is needed to build, not sur if use later
        ln -sfn  /usr/include/eigen3/ /usr/include/eigen3/include
}


src_configure() {
        local myeconfargs=(
                #--disable-optim
                --with-boost="${EPREFIX}/usr/$(get_libdir)/"
                --with-boost-thread="${EPREFIX}/usr/$(get_libdir)/libboost_thread.so"
                --with-boost-system="${EPREFIX}/usr/$(get_libdir)/libboost_system.so"
                --with-bam="${EPREFIX}/usr/"
                --with-eigen="/usr/include/eigen3/"
                $(use_enable debug)
        )
        autotools-utils_src_configure
}