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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit eutils
DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads"
HOMEPAGE="http://sb.cs.cmu.edu/seecer/"
SRC_URI="
http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz
http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf"
LICENSE="GPL-3"
SLOT="0"
IUSE=""
KEYWORDS="~amd64"
# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime
# seems jellyfish-2 does not accept same commandline arguments
DEPEND="
sci-libs/gsl:0=
sci-biology/seqan:0="
RDEPEND="${DEPEND}
=sci-biology/jellyfish-1.1.11"
S="${S}"/SEECER
PATCHES=(
"${FILESDIR}"/remove-hardcoded-paths.patch
)
src_prepare(){
# http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html
cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die
default
}
src_install(){
dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh
dodoc README "${DISTDIR}"/"${PN}"-manual.pdf
}
pkg_postinst(){
einfo "Note that the default kmer size 17 is terribly suboptimal, use k=31 instead"
}
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