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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
inherit eutils
MY_PV=${PV//\./-}
DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
HOMEPAGE="http://repeatmasker.org/"
SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
LICENSE="OSL-2.1"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=">=dev-lang/perl-5.8"
RDEPEND="
sci-biology/rmblast
>=sci-biology/trf-4.0.4
sci-biology/repeatmasker-libraries
sci-biology/phrap"
# dev-perl/Text-Soundex see bug #566740
S="${WORKDIR}/RepeatMasker"
src_prepare(){
epatch "${FILESDIR}"/"${P}"__configure.patch
}
src_configure() {
# The below is wrong as it causes:
# Enter path [ /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
# -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
sed -i -e 's/system( "clear" );//' "${S}/configure" || die
mkdir -p "${D}"/usr/share/repeatmasker/Libraries/ || die
#
# the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
# item does not get installed
echo ">blah\natgc" > "${D}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
echo "
env
${S}
/opt/bin
1
/usr/bin
Y
2
/usr/bin
Y
4
/usr/bin
Y
5" | "${S}/configure" || die "configure failed"
sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
-e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/Libraries/\1"|' \
-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
}
# configure failed to 'cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm'
# replace also /u1/local/bin/perl with proper Gentoo PATH
src_install() {
exeinto /usr/share/${PN}
for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
doexe $i
dosym /usr/share/${PN}/$i /usr/bin/$i
done
dodir /usr/share/${PN}/lib
insinto /usr/share/${PN}/lib
doins "${S}"/*.pm "${S}"/Libraries/*.pm
# zap the supposedly misplaced RepeatAnnotationData.pm file
rm -rf "${S}"/Libraries/*.pm || die
# if sci-biology/repeatmasker-libraries is installed prevent file collision
# and do NOT install Libraries/RepeatMaskerLib.embl file which contains
# a limited version of the file: 20110419-min
rm -rf Libraries/RepeatMaskerLib.embl || die
insinto /usr/share/${PN}
doins -r util Matrices Libraries *.help
keepdir /usr/share/${PN}/Libraries
dodoc README INSTALL *.help
}
pkg_postinst(){
einfo "RepeatMasker provides bundled human repeats database"
einfo "from Dfam-1.0 database www.dfam.org"
einfo "You can configure which search search engine is to be used and"
einfo "PATHs to the search binaries are defined in"
einfo "/usr/share/${PN}/lib/RepeatMaskerConfig.pm"
einfo "Supported search engines are:"
einfo "cross_match from sci-biology/phrap"
einfo "rmblast from sci-biology/rmblast"
einfo "nhmmer from >=sci-biology/hmmer-3.1"
einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"
}
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