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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit eutils toolchain-funcs
DESCRIPTION="Trimpoly and mdust for trimming and validation of ESTs/DNA sequences"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
for i in seqcl_scripts mdust trimpoly; do
SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/${i}.tar.gz -> ${i}-${PV}.tar.gz"
done
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
dev-lang/perl
sci-biology/ncbi-tools"
RDEPEND="${DEPEND}"
S=${WORKDIR}
src_prepare() {
# disable the necessity to install Mailer.pm with this tool
einfo "Disabling mailer feature within seqclean"
sed -i 's/use Mailer;/#use Mailer;/' "${S}"/"${PN}"/"${PN}" || die
epatch "${FILESDIR}"/${P}-build.patch
tc-export CC CXX
}
src_compile() {
for i in mdust trimpoly; do
LDLFAGS="${LDFLAGS}" \
emake -C "${S}"/${i}
done
}
src_install() {
dobin seqclean/{seqclean,cln2qual,bin/seqclean.psx}
newdoc seqclean/README README.seqclean
for i in mdust trimpoly; do
dobin ${i}/${i}
done
einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own"
einfo "fasta file with vector sequences you want to remove from sequencing"
einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html"
}
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