commit: 62c5ffc75e7cea39f2488c7567ea47808c57b8f8 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Nov 24 19:27:44 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Nov 24 19:27:44 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=62c5ffc7
sci-biology/repeatmasker: heavily patch configure to return error codes and die upon error; add more DEPENDencies Package-Manager: portage-2.2.18 sci-biology/repeatmasker/ChangeLog | 10 ++ sci-biology/repeatmasker/files/configure.patch | 122 +++++++++++++++++++++ sci-biology/repeatmasker/metadata.xml | 5 + .../repeatmasker/repeatmasker-4.0.1-r1.ebuild | 100 +++++++++++++++++ 4 files changed, 237 insertions(+) diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog new file mode 100644 index 0000000..67ed4e6 --- /dev/null +++ b/sci-biology/repeatmasker/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/repeatmasker +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Id$ + +*repeatmasker-4.0.1-r1 (24 Nov 2015) + + 24 Nov 2015; Martin Mokrejs <[email protected]> + +files/configure.patch, +metadata.xml, +repeatmasker-4.0.1-r1.ebuild: + sci-biology/repeatmasker: heavily patch configure to return error codes and + die upon error; add more DEPENDencies diff --git a/sci-biology/repeatmasker/files/configure.patch b/sci-biology/repeatmasker/files/configure.patch new file mode 100644 index 0000000..0b8a75c --- /dev/null +++ b/sci-biology/repeatmasker/files/configure.patch @@ -0,0 +1,122 @@ +--- configure.ori 2013-02-21 02:32:30.000000000 +0100 ++++ configure 2015-11-24 19:54:50.630202150 +0100 +@@ -253,17 +253,16 @@ + close INVERS; + } + else { +- print "\nYour RepeatMasker installation is missing a library file.\n" ++ die "\nYour RepeatMasker installation is missing a library file.\n" + . "RepeatMasker requires a minimal set of library sequences to run\n" + . "properly. Please check that all files were extracted from the\n" + . "distribution before re-running the configure program.\n\n"; +- exit; + } + + print "\n -- Building monolithic RM database..."; + system( + "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null" +-); ++) and die "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!"; + + ## + ## TRF location +@@ -475,7 +474,7 @@ + } + close IN; + close OUT; +- system( "mv $configFile.tmp $configFile" ); ++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; + } + + } +@@ -607,15 +606,15 @@ + } + close IN; + close OUT; +- system( "mv $configFile.tmp $configFile" ); ++ system( "mv $configFile.tmp $configFile" ) and die "Faled to mv $configFile.tmp $configFile: $!"; + + # Freeze RM and RMPep libraries for RepeatModeler use among others + my $rmLocation = "$FindBin::Bin"; + print "Building RMBlast frozen libraries..\n"; + system( "$pgLocation/makeblastdb -dbtype nucl -in " +- . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ); ++ . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype nucl -in $rmLocation/Libraries/RepeatMasker.lib failed: $!"; + system( "$pgLocation/makeblastdb -dbtype prot -in " +- . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ); ++ . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib failed with: $!"; + + my $pgDefault = &promptScreen( + "", +@@ -682,15 +681,15 @@ + } + close IN; + close OUT; +- system( "mv $configFile.tmp $configFile" ); ++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; + + # Freeze RM and RMPep libraries + my $rmLocation = "$FindBin::Bin"; + print "Building WUBlast/ABBlast frozen libraries..\n"; + system( "$wuLocation/xdformat -n -I " +- . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ); ++ . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed with: $!"; + system( "$wuLocation/xdformat -p -I " +- . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ); ++ . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with: $!"; + + my $wuDefault = &promptScreen( + "", +@@ -748,7 +747,7 @@ + } + } + else { +- print "ERROR: Could not find nhmmer program in this directory!\n"; ++ print "ERROR: Could not find nhmmer program in '$location' directory!\n"; + } + if ( $goodParam == 0 ) { + print "<PRESS ENTER TO CONTINUE>\n"; +@@ -773,7 +772,7 @@ + } + close IN; + close OUT; +- system( "mv $configFile.tmp $configFile" ); ++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; + + my $default = &promptScreen( + "", +@@ -827,7 +826,7 @@ + } + close IN; + close OUT; +- system( "mv $configFile.tmp $configFile" ); ++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; + + my $deDefault = &promptScreen( + "", +@@ -863,9 +862,6 @@ + + my $answer = undef; + +- # Clear the screen +- system( "clear" ); +- + print "\n\n\n"; + print $screenText; + my $numLines = ( $screenText =~ s/(\n)/$1/g ); +--- configure.ori 2015-11-24 20:10:58.640204679 +0100 ++++ configure 2015-11-24 20:11:00.970204685 +0100 +@@ -728,11 +728,12 @@ + # HMMER 3.0dev (March 2010); http://hmmer.org/ + # HMMER 3.1dev_0.33 (July 2012); http://hmmer.org + # HMMER hmmer3.1-snap20120830 (August 2012); http://hmmer.org/ ++ # HMMER 3.1b2 (February 2015); http://hmmer.org/ + while ( $result =~ /([^\n\r]*)[\n\r]/ig ) { + my $line = $1; + + if ( $line =~ /^#\s+HMMER\s+(\d+\.\d+)((dev)?(_\d+\.\d+)?\s+\(.*\)).*/ +- || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ ) ++ || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ || $line =~ /^#\s+HMMER\s+(\d+\.\d+).*/) + { + if ( $1 >= 3.1 ) { + $goodParam = 1; diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/repeatmasker/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> 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 0000000..9507e23 --- /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"; +}
