1 files changed, 102 insertions, 0 deletions
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
new file mode 100644
index 000000000..86be5affe
--- /dev/null
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r2.ebuild
@@ -0,0 +1,102 @@
+# 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 $i || die
+		dosym /usr/share/${PN}/$i /usr/bin/$i || die
+	done
+
+	dodir /usr/share/${PN}/lib
+	insinto /usr/share/${PN}/lib
+	doins "${S}"/*.pm "${S}"/Libraries/*.pm
+	rm -rf "${S}"/Libraries/*.pm # zap the supposedly misplaced RepeatAnnotationData.pm file
+
+	# if sci-biology/repeatmasker-libraries is installed prevent file collision
+	# and do NOT install Libraries/RepeatMaskerLib.embl file which contains
+	# a limited version of the file: 20110419-min
+	rm -rf Libraries/RepeatMaskerLib.embl
+	insinto /usr/share/${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"
+}