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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
DESCRIPTION="Noise removal from pyrosequenced amplicons"
HOMEPAGE="http://code.google.com/p/ampliconnoise/"
SRC_URI="
http://ampliconnoise.googlecode.com/files/AmpliconNoiseV${PV}.tar.gz
http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz
http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"
LICENSE="LGPL-3"
SLOT="0"
KEYWORDS=""
IUSE="mpi"
RDEPEND="
mpi? ( virtual/mpi )
sci-libs/gsl
sci-biology/mafft
sci-biology/usearch-bin
dev-haskell/biosff || ( sci-biology/flower )"
# sci-biology/flower::haskell installs renamed binaries to avoid file collision
# unfortunately flower executable from the two packages
# dev-haskell/biosff::science vs. sci-biology/flower::haskell
# do not offer same cmdline options (upstream did not sync the two packages)
S="${WORKDIR}/AmpliconNoiseV1.27"
src_compile(){
# FIXME: the Makefile forcibly calls 'mpicc'
emake
cd ../DiversityEstimates || die
emake
}
src_install(){
default
dodoc "${WORKDIR}"/TutorialV1.22/Tutorial.ppt "${WORKDIR}"/TutorialV1.22/SmallTwins.* Doc.pdf
mv bin "${DESTDIR}/${EPREFIX}"/usr/ || die
insinto /usr/share/"${PN}"/scripts
doins Scripts/*.pl Scripts/*.sh
}
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