RepeatMasker-3.1.6.ebuild

RepeatMasker-3.1.6.ebuild (text/plain), 1.79 KB, created by Andrey Kislyuk (RETIRED) on 2006-11-12 14:33:10 UTC

# Copyright 1999-2005 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2

inherit versionator

MY_PV=$(replace_all_version_separators '-')

DESCRIPTION="\
RepeatMasker is a program that screens DNA sequences for interspersed repeats
and low complexity DNA sequences. The output of the program is a detailed
annotation of the repeats that are present in the query sequence as well as a
modified version of the query sequence in which all the annotated repeats have
been masked (default: replaced by Ns). It requiers an executable called
cross_match to run. Cross_match can be found in another application called
Phrap. Phrap has limited availablty."
HOMEPAGE="http://repeatmasker.org/"
SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
LICENSE="unknown"
IUSE=""
SLOT="0"
KEYWORDS="~x86"

DEPEND=">=dev-lang/perl-5.8.0"
RDEPEND="${DEPEND}
	sci-biology/crossmatch
	sci-biology/RepeatMaskerLibraries"


S=${WORKDIR}/RepeatMasker

src_compile() {
	cat << EOF > configure.commands

/usr/bin
/usr/share/${PN}
1
/usr/bin
Y
4
EOF

	einfo "Configuring repeatmasker. This shouldn't take more than a second."
	perl ./configure < configure.commands > /dev/null || die
	sed -i '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' "${S}/RepeatMaskerConfig.pm"
}

src_install() {
	dobin DateRepeats ProcessRepeats RepeatMasker util/*
	dodir /usr/share/${PN}/lib
	insinto /usr/share/${PN}/lib
	doins "${S}/"*".pm"
	dodoc README INSTALL repeatmasker.help daterepeats.help

	echo 'COLON_SEPARATED=PERL5LIB' > ${S}/99${PN}
	echo "PERL5LIB=\"/usr/share/${PN}/lib\"" >> ${S}/99${PN}
	doenvd ${S}/99${PN}

	keepdir /usr/share/${PN}/{Libraries,Matrices/{crossmatch,wublast/aa}}
	for i in crossmatch wublast/aa; do
		insinto /usr/share/${PN}/Matrices/${i}
		doins ${S}/Matrices/${i}/*
	done
}