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# Copyright 1999-2006 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
# http://bugs.gentoo.org/show_bug.cgi?id=157827
DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx"
LICENSE="Artistic"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
SLOT="0"
IUSE=""
KEYWORDS="~x86"
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
RESTRICT="nomirror"
DEPEND=""
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;/' ${S}/seqclean/seqclean
sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' ${S}/zmsort/zmsort.cpp
# TODO: fix errors in nrcl, pvmsx
for i in cdbfasta mdust psx sclust tclust trimpoly zmsort; do
sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' ${S}/${i}/Makefile
(cd ${S}/${i}; emake) || die
done
}
src_install() {
dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
for i in mdust psx sclust tclust trimpoly zmsort; do dobin ${i}/${i}; done
}
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