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# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do
SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz"
done
LICENSE="Artistic"
SLOT="0"
IUSE="pvm"
KEYWORDS="~x86"
DEPEND="pvm? ( sys-cluster/pvm )"
RDEPEND="${DEPEND}"
S=${WORKDIR}
src_unpack() {
unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz
for i in nrcl sclust tclust zmsort psx pvmsx; do
mkdir "${S}"/${i}
cd "${S}"/${i}
unpack ${i}.tar.gz
done
}
src_compile() {
sed -i 's/use Mailer;/#use Mailer;/' seqclean/seqclean
sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' zmsort/zmsort.cpp
# TODO: fix error in nrcl
for i in cdbfasta mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' \
${i}/Makefile
cd "${S}/${i}" || die "cd ${i} failed"
emake || die "emake failed in ${i}"
done
}
src_install() {
dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
for i in mdust psx sclust tclust trimpoly zmsort $(use pvm && echo pvmsx); do
dobin ${i}/${i}
done
for i in cdbfasta seqclean; do
newdoc ${i}/README README.${i}
done
}
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