commit: 777780e24faa006c5883307c0dadd31cab8cecd8 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 29 16:24:12 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Mar 29 16:24:12 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=777780e2
sci-biology/repeatmasker: rewamp configuration code The changes are partly based on https://github.com/gentoo/sci/pull/580 from Michael Schubert but it seems we could figure out the paths to binaries automatically using `which`. Block between the USE options and allow only a single to be enabled, that is what configure requires, otherwise it enters a loop. The hmmer is the default in configure and preferred. Tested with `USE="hmmer -wublast -phrap -rmblast"` and other combinations while only one is allowed. If users have wublast/abblast/rmblast/crossmatch in the PATHS we just pick it. `which` returns a '.' (dot) if a binary was not found, we need to zap it otherwise configure enters a loop. In the end, one can get: Add a Search Engine: 1. CrossMatch: [ Configured ] 2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured ] 3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ] 4. HMMER3.1 & DFAM: [ Configured, Default ] 5. Done properly written into /usr/lib64/perl5/vendor_perl/5.28.0/RepeatMaskerConfig.pm Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> .../files/repeatmasker-4.0.6__configure.patch | 4 +- sci-biology/repeatmasker/metadata.xml | 6 + .../repeatmasker/repeatmasker-4.0.6-r3.ebuild | 111 ---------------- .../repeatmasker/repeatmasker-4.0.6-r4.ebuild | 142 +++++++++++++++++++++ .../repeatmasker/repeatmasker-4.0.8-r1.ebuild | 111 ---------------- .../repeatmasker/repeatmasker-4.0.8-r2.ebuild | 142 +++++++++++++++++++++ 6 files changed, 292 insertions(+), 224 deletions(-) diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch index e4042190f..c1e0cfb55 100644 --- a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch +++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch @@ -1,5 +1,5 @@ ---- configure.ori 2015-11-24 20:56:46.000000000 +0100 -+++ configure 2015-11-24 20:59:58.000000000 +0100 +--- RepeatMasker/configure.ori 2015-11-24 20:56:46.000000000 +0100 ++++ RepeatMasker/configure 2015-11-24 20:59:58.000000000 +0100 @@ -253,17 +253,16 @@ close INVERS; } diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml index 8417d1580..de382fa16 100644 --- a/sci-biology/repeatmasker/metadata.xml +++ b/sci-biology/repeatmasker/metadata.xml @@ -5,4 +5,10 @@ <email>[email protected]</email> <name>Gentoo Biology Project</name> </maintainer> + <use> + <flag name="phrap">Use cross_match search engine as default</flag> + <flag name="rmblast">Use RM-BLAST search engine as default</flag> + <flag name="hmmer">Use HMMER search engine as default</flag> + <flag name="wublast">Use wublast or abblast search engine as default</flag> + </use> </pkgmetadata> diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild deleted file mode 100644 index d41784eb7..000000000 --- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild +++ /dev/null @@ -1,111 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils perl-module - -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=" - dev-perl/Text-Soundex - sci-biology/phrap - <=sci-biology/repeatmasker-libraries-20160829 - sci-biology/rmblast - !sci-biology/trf - >=sci-biology/trf-bin-4.0.4 -" - -S="${WORKDIR}/RepeatMasker" - -PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) - -src_configure() { - sed \ - -e "s#/usr/bin/which#which#g" \ - -e "s#/usr/bin/perl#perl#g" \ - -i "${S}"/configure || die - perl_set_version - insinto ${VENDOR_LIB} - sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die - # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die - # - # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' - # item does not get installed - echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die - # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools - echo " -env -${S} -${EPREFIX}/opt/trf/bin -1 -${EPREFIX}/usr/bin -Y -2 -${EPREFIX}/usr/bin -Y -4 -${EPREFIX}/usr/bin -Y -5" | "${S}"/configure || die "configure failed" - sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \ - -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \ - -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${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 $i - dosym ../share/${PN}/$i /usr/bin/$i - done - - perl_set_version - insinto "${VENDOR_LIB}" - doins "${S}"/*.pm "${S}"/Libraries/*.pm - # zap the supposedly misplaced RepeatAnnotationData.pm file - rm -r "${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 -r 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 "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm" - einfo "Supported search engines are:" - optfeature "cross_match" sci-biology/phrap - optfeature "rmblast" sci-biology/rmblast - optfeature "nhmmer" \>=sci-biology/hmmer-3.1 - einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"; - einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last" - einfo "version compatible with <repeatmasker-4.0.7" -} diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild new file mode 100644 index 000000000..8216bfe7f --- /dev/null +++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r4.ebuild @@ -0,0 +1,142 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils perl-module + +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="phrap rmblast hmmer wublast" +# RepeatMaskerConfig.pm says: +# Default search tool can be one of "hmmer", "crossmatch", "wublast", "decypher" or "ncbi". +# Upstream uses "hmmer" as the default. + +DEPEND=">=dev-lang/perl-5.8" +RDEPEND=" + <=sci-biology/repeatmasker-libraries-20160829 + dev-perl/Text-Soundex + phrap? ( !hmmer? ( !rmblast? ( !wublast? ( sci-biology/phrap ) ) ) ) + rmblast? ( !hmmer? ( !phrap? ( !wublast? ( sci-biology/rmblast ) ) ) ) + hmmer? ( !phrap? ( !wublast? ( !rmblast? ( sci-biology/hmmer ) ) ) ) + !sci-biology/trf + >=sci-biology/trf-bin-4.0.4 +" +# wublast? ( sci-biology/wublast || sci-biology/abblast ) +# ncbi? ( would that be ncbi-tools++ or ncbi-blast+ ) ??? + +S="${WORKDIR}/RepeatMasker" + +PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) + +src_configure() { + sed \ + -e "s#/usr/bin/which#which#g" \ + -e "s#/usr/bin/perl#perl#g" \ + -i "${S}"/configure || die + perl_set_version + insinto ${VENDOR_LIB} + sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die + # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die + # + # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' + # item does not get installed + echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die + # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools + # + local my_crossmatch=`which cross_match 2>/dev/null` + local my_rmblastn=`which rmblastn 2>/dev/null` + local my_hmmer=`which nhmmscan 2>/dev/null` + local my_wublast=`which xdformat 2>/dev/null` # actually configure looks for 'setdb' executable + # configure is inconsistent at first, we must pass even a wrong path for cross_match, rmblastn, hmmer otherwise it enters a loop + # but, for wublast we must pass in an empty string otherwise it looks for 'setdb' executable in the non-existing directory and enters a loop + if [ "$my_crossmatch" != '.' ]; then local crossmatchdir=`dirname "$my_crossmatch"` else local crossmatchdir="${EPREFIX}/usr/bin"; fi + if [ "$my_rmblastn" != '.' ]; then local rmblastdir=`dirname "$my_rmblastn"` else local rmblastdir="${EPREFIX}/usr/bin"; fi + if [ "$my_hmmer" != '.' ]; then local hmmerdir=`dirname "$my_hmmer"` else local hmmerdir="${EPREFIX}/usr/bin"; fi + if [ "$my_wublast" != '.' ]; then local wublastdir=`dirname "$my_wublast"` else local wublastdir=""; fi + echo "crossmatchdir=${crossmatchdir} rmblastdir=${rmblastdir} wublastdir=${wublastdir} hmmerdir=${hmmerdir}" + # pick the preferred-one + local CONF=( x env ${S} "${EPREFIX}"/opt/bin ) + if use phrap; then + CONF+=( 1 "${crossmatchdir}" Y ) + else + CONF+=( 1 "${crossmatchdir}" N ) + fi + if use rmblast; then + CONF+=( 2 "${rmblastdir}" Y ) + else + CONF+=( 2 "${rmblastdir}" N ) + fi + if use wublast; then + # no ebuild available but pick anything from PATH + CONF+=( 3 "${wublastdir}" Y ) + else + CONF+=( 3 "${wublastdir}" N ) + fi + if use hmmer; then + CONF+=( 4 "${hmmerdir}" Y ) + else + CONF+=( 4 "${hmmerdir}" N ) + fi + CONF+=( 5 ) + echo "Will feed configure with: ${CONF[@]}" + printf '%s\n' "${CONF[@]}" | "${S}/configure" || die "configure failed" + + sed -i -e "/use lib/s|\"\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib|" \ + -e "/use lib/s|\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib\"|" \ + -e "/\$REPEATMASKER_DIR/ s|\$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \ + "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die +} + +src_install() { + exeinto /usr/share/${PN} + for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do + doexe $i + dosym ../share/${PN}/$i /usr/bin/$i + done + + perl_set_version + insinto "${VENDOR_LIB}" + doins "${S}"/*.pm "${S}"/Libraries/*.pm + # zap the supposedly misplaced RepeatAnnotationData.pm file + rm -r "${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 -r 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(){ + cd "${S}" || die + einfo "RepeatMasker provides bundled human repeats database from" + einfo " Dfam-1.0 database www.dfam.org" + einfo "You can configure which search search engine is to be used and" + einfo "Current default search engine defined in" + einfo " ${EPREFIX}${VENDOR_LIB}/RepeatMaskerConfig.pm is:" + einfo `grep 'DEFAULT_SEARCH_ENGINE =' RepeatMaskerConfig.pm` + einfo "\nSupported search engines are:" + optfeature "cross_match" sci-biology/phrap + optfeature "rmblast" sci-biology/rmblast + optfeature "nhmmer" \>=sci-biology/hmmer-3.1 + einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"; + einfo "\nThe repeatmasker-libraries-20160829 (RepBase 21.12) was the last" + einfo "version compatible with <repeatmasker-4.0.7" +} diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild deleted file mode 100644 index 9b4af2312..000000000 --- a/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild +++ /dev/null @@ -1,111 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit eutils perl-module - -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=" - dev-perl/Text-Soundex - sci-biology/phrap - >sci-biology/repeatmasker-libraries-20160829 - sci-biology/rmblast - !sci-biology/trf - >=sci-biology/trf-bin-4.0.4 -" - -S="${WORKDIR}/RepeatMasker" - -PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) - -src_configure() { - sed \ - -e "s#/usr/bin/which#which#g" \ - -e "s#/usr/bin/perl#perl#g" \ - -i "${S}"/configure || die - perl_set_version - insinto ${VENDOR_LIB} - sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die - # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die - # - # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' - # item does not get installed - echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die - # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools - echo " -env -${S} -${EPREFIX}/opt/trf/bin -1 -${EPREFIX}/usr/bin -Y -2 -${EPREFIX}/usr/bin -Y -4 -${EPREFIX}/usr/bin -Y -5" | "${S}"/configure || die "configure failed" - sed -i -e "s|use lib $FindBin::RealBin;|use lib ${EPREFIX}/usr/share/${PN}/lib;|" \ - -e "s|.*\(taxonomy.dat\)|${EPREFIX}/usr/share/${PN}/Libraries/\1|" \ - -e "/$REPEATMASKER_DIR/ s|$FindBin::RealBin|${EPREFIX}/usr/share/${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 $i - dosym ../share/${PN}/$i /usr/bin/$i - done - - perl_set_version - insinto "${VENDOR_LIB}" - doins "${S}"/*.pm "${S}"/Libraries/*.pm - # zap the supposedly misplaced RepeatAnnotationData.pm file - rm -r "${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 -r Libraries/RepeatMaskerLib.embl || die - insinto /usr/share/${PN} - doins -r util Matrices Libraries *.help - keepdir /usr/share/${PN}/Libraries - - dodoc README.md 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 "${EPREFIX}/usr/share/${PN}/lib/RepeatMaskerConfig.pm" - einfo "Supported search engines are:" - optfeature "cross_match" sci-biology/phrap - optfeature "rmblast" sci-biology/rmblast - optfeature "nhmmer" \>=sci-biology/hmmer-3.1 - einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"; - einfo "repeatmasker-libraries-20160829 (RepBase 21.12) was the last" - einfo "version compatible with <repeatmasker-4.0.7" -} diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild new file mode 100644 index 000000000..02700ba2b --- /dev/null +++ b/sci-biology/repeatmasker/repeatmasker-4.0.8-r2.ebuild @@ -0,0 +1,142 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit eutils perl-module + +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="phrap rmblast hmmer wublast" +# RepeatMaskerConfig.pm says: +# Default search tool can be one of "hmmer", "crossmatch", "wublast", "decypher" or "ncbi". +# Upstream uses "hmmer" as the default. + +DEPEND=">=dev-lang/perl-5.8" +RDEPEND=" + >sci-biology/repeatmasker-libraries-20160829 + dev-perl/Text-Soundex + phrap? ( !hmmer? ( !rmblast? ( !wublast? ( sci-biology/phrap ) ) ) ) + rmblast? ( !hmmer? ( !phrap? ( !wublast? ( sci-biology/rmblast ) ) ) ) + hmmer? ( !phrap? ( !wublast? ( !rmblast? ( sci-biology/hmmer ) ) ) ) + !sci-biology/trf + >=sci-biology/trf-bin-4.0.4 +" +# wublast? ( sci-biology/wublast || sci-biology/abblast ) +# ncbi? ( would that be ncbi-tools++ or ncbi-blast+ ) ??? + +S="${WORKDIR}/RepeatMasker" + +PATCHES=( "${FILESDIR}"/"${P}"__configure.patch ) + +src_configure() { + sed \ + -e "s#/usr/bin/which#which#g" \ + -e "s#/usr/bin/perl#perl#g" \ + -i "${S}"/configure || die + perl_set_version + insinto ${VENDOR_LIB} + sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die + # 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 "${ED}"/usr/share/repeatmasker/Libraries/ || die + # + # the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah' + # item does not get installed + echo ">blah\natgc" > "${ED}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die + # below try to define paths to trf, cross_match, rmblast and nhmmer as search tools + # + local my_crossmatch=`which cross_match 2>/dev/null` + local my_rmblastn=`which rmblastn 2>/dev/null` + local my_hmmer=`which nhmmscan 2>/dev/null` + local my_wublast=`which xdformat 2>/dev/null` # actually configure looks for 'setdb' executable + # configure is inconsistent at first, we must pass even a wrong path for cross_match, rmblastn, hmmer otherwise it enters a loop + # but, for wublast we must pass in an empty string otherwise it looks for 'setdb' executable in the non-existing directory and enters a loop + if [ "$my_crossmatch" != '.' ]; then local crossmatchdir=`dirname "$my_crossmatch"` else local crossmatchdir="${EPREFIX}/usr/bin"; fi + if [ "$my_rmblastn" != '.' ]; then local rmblastdir=`dirname "$my_rmblastn"` else local rmblastdir="${EPREFIX}/usr/bin"; fi + if [ "$my_hmmer" != '.' ]; then local hmmerdir=`dirname "$my_hmmer"` else local hmmerdir="${EPREFIX}/usr/bin"; fi + if [ "$my_wublast" != '.' ]; then local wublastdir=`dirname "$my_wublast"` else local wublastdir=""; fi + echo "crossmatchdir=${crossmatchdir} rmblastdir=${rmblastdir} wublastdir=${wublastdir} hmmerdir=${hmmerdir}" + # pick the preferred-one + local CONF=( x env ${S} "${EPREFIX}"/opt/bin ) + if use phrap; then + CONF+=( 1 "${crossmatchdir}" Y ) + else + CONF+=( 1 "${crossmatchdir}" N ) + fi + if use rmblast; then + CONF+=( 2 "${rmblastdir}" Y ) + else + CONF+=( 2 "${rmblastdir}" N ) + fi + if use wublast; then + # no ebuild available but pick anything from PATH + CONF+=( 3 "${wublastdir}" Y ) + else + CONF+=( 3 "${wublastdir}" N ) + fi + if use hmmer; then + CONF+=( 4 "${hmmerdir}" Y ) + else + CONF+=( 4 "${hmmerdir}" N ) + fi + CONF+=( 5 ) + echo "Will feed configure with: ${CONF[@]}" + printf '%s\n' "${CONF[@]}" | "${S}/configure" || die "configure failed" + + sed -i -e "/use lib/s|\"\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib|" \ + -e "/use lib/s|\$FindBin::RealBin|\"${EPREFIX}/usr/share/${PN}/lib\"|" \ + -e "/\$REPEATMASKER_DIR/ s|\$FindBin::RealBin|${EPREFIX}/usr/share/${PN}|" \ + "${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die +} + +src_install() { + exeinto /usr/share/${PN} + for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do + doexe $i + dosym ../share/${PN}/$i /usr/bin/$i + done + + perl_set_version + insinto "${VENDOR_LIB}" + doins "${S}"/*.pm "${S}"/Libraries/*.pm + # zap the supposedly misplaced RepeatAnnotationData.pm file + rm -r "${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 -r Libraries/RepeatMaskerLib.embl || die + insinto /usr/share/${PN} + doins -r util Matrices Libraries *.help + keepdir /usr/share/${PN}/Libraries + + dodoc README.md INSTALL *.help +} + +pkg_postinst(){ + cd "${S}" || die + einfo "RepeatMasker provides bundled human repeats database from" + einfo " Dfam-1.0 database www.dfam.org" + einfo "You can configure which search search engine is to be used and" + einfo "Current default search engine defined in" + einfo " ${EPREFIX}${VENDOR_LIB}/RepeatMaskerConfig.pm is:" + einfo `grep 'DEFAULT_SEARCH_ENGINE =' RepeatMaskerConfig.pm` + einfo "\nSupported search engines are:" + optfeature "cross_match" sci-biology/phrap + optfeature "rmblast" sci-biology/rmblast + optfeature "nhmmer" \>=sci-biology/hmmer-3.1 + einfo "abblast/wublast from http://blast.advbiocomp.com/licensing"; + einfo "\nThe repeatmasker-libraries-20160829 (RepBase 21.12) was the last" + einfo "version compatible with <repeatmasker-4.0.7" +}
