diff options
Diffstat (limited to 'sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild')
-rw-r--r-- | sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild | 100 |
1 files changed, 100 insertions, 0 deletions
diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild new file mode 100644 index 000000000..9507e23cd --- /dev/null +++ b/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild @@ -0,0 +1,100 @@ +# 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}"/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/'${PN}'/\1"|' \ + -e '/$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 "${S}"/*.pm || die + + # if sci-biology/repeatmasker-libraries is installed prevent file collision + # and do NOT install Libraries/RepeatMaskerLib.embl file which contains + # a limited version of the file: 20110419-min + rm -rf Libraries/RepeatMaskerLib.embl + insinto /usr/share/${PN} + doins -r util Matrices Libraries taxonomy.dat *.help || die + 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 in 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" +} |