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# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/glimmerhmm/glimmerhmm-3.0.1.ebuild,v 1.2 2008/09/07 14:37:31 weaver Exp $
MY_P=GlimmerHMM
DESCRIPTION="An eukaryotic gene finding system from TIGR"
HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/"
SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
LICENSE="Artistic"
SLOT="0"
IUSE=""
KEYWORDS="~x86"
DEPEND=""
RDEPEND=""
S="${WORKDIR}/${MY_P}"
src_compile() {
sed -i -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/share/'${PN}'/training_utils"|' \
-e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' train/trainGlimmerHMM || die "sed failed"
sed -i 's/^CFLAGS[ ]*=.*//' */makefile
cd sources
emake || die "emake failed in sources"
cd "${S}/train" || die "failed to cd"
emake || die "emake failed in train"
}
src_install() {
dobin sources/glimmerhmm train/trainGlimmerHMM
dodir /usr/share/${PN}/{lib,models,training_utils}
insinto /usr/share/${PN}/lib
doins train/*.pm
insinto /usr/share/${PN}/models
doins -r trained_dir/*
insinto /usr/share/${PN}/training_utils
insopts -m755
doins train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}
dodoc README.first train/readme.train
}
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