commit: b42d6fd23f783fe21761e20fceb2291a21de61c0 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Nov 30 16:12:25 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Nov 30 16:12:25 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b42d6fd2
sci-biology/repeatmasker: version bump, escape >= to avoid shell redirect This introduces new repeatmasker-4.0.8 which can use repeatmasker-libraries releasded after 20160829. Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> Package-Manager: Portage-2.3.51, Repoman-2.3.11 .../files/repeatmasker-4.0.8__configure.patch | 118 +++++++++++++++++++++ .../repeatmasker/repeatmasker-4.0.6-r3.ebuild | 2 +- ....0.6-r3.ebuild => repeatmasker-4.0.8-r1.ebuild} | 8 +- 3 files changed, 123 insertions(+), 5 deletions(-) diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch new file mode 100644 index 000000000..728bb75b1 --- /dev/null +++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.8__configure.patch @@ -0,0 +1,118 @@ +--- RepeatMasker/configure.ori 2018-11-30 16:50:39.918872258 +0100 ++++ RepeatMasker/configure 2018-11-30 17:00:33.255400144 +0100 +@@ -78,11 +78,10 @@ + ## unqualified from another installation directory. + ## + if ( cwd() ne $FindBin::RealBin ) { +- print "\n The RepeatMasker configure script must be run from\n" ++ die "\n The RepeatMasker configure script must be run from\n" + . " inside the RepeatMasker installation directory:\n\n" + . " $FindBin::RealBin\n\n" + . " Perhaps this is not the \"configure\" you are looking for?\n\n"; +- exit; + } + + ## +@@ -228,12 +227,12 @@ + print "\n -- Building FASTA database..."; + system( + "$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: $!"; + + ## Uncompress taxonomy.dat + if ( -s "$rmLocation/Libraries/taxonomy.dat.gz" ) { + print "\n -- Uncompressing taxonomy.dat..."; +- system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" ); ++ system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" ) and die "gunzip $rmLocation/Libraries/taxonomy.dat.gz failed with: $!"; + } + + ## +@@ -278,7 +277,7 @@ + } while ( $goodParam != 1 ); + + # Initialize config from template. +-system( "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm" ); ++system( "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm" ) and die "cp RepeatMaskerConfig.tmpl RepeatMaskerConfig.pm failed with: $!"; + + # Make changes to file. + my $configFile = "RepeatMaskerConfig.pm"; +@@ -290,7 +289,7 @@ + } + close IN; + close OUT; +-system( "mv $configFile.tmp $configFile" ); ++system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; + + ## + ## Search Engine Configuration +@@ -452,7 +451,7 @@ + } + close IN; + close OUT; +- system( "mv $configFile.tmp $configFile" ); ++ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; + } + + } +@@ -590,9 +589,9 @@ + 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( + "", +@@ -665,9 +664,9 @@ + 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 $wuDefault = &promptScreen( + "", +@@ -733,7 +732,7 @@ + } + } + else { +- print "ERROR: Could not find nhmmer program in this directory!\n"; ++ print "ERROR: Could not find nhmmer program in '$location' directory!\n"; + } + } + +@@ -753,7 +752,7 @@ + } + 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( + "", +@@ -807,7 +806,7 @@ + } + 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( + "", +@@ -843,9 +842,6 @@ + + my $answer = undef; + +- # Clear the screen +- system( "clear" ); +- + print "\n\n\n"; + print $screenText; + my $numLines = ( $screenText =~ s/(\n)/$1/g ); diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild index 2ff6c8be6..d41784eb7 100644 --- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild +++ b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild @@ -104,7 +104,7 @@ pkg_postinst(){ einfo "Supported search engines are:" optfeature "cross_match" sci-biology/phrap optfeature "rmblast" sci-biology/rmblast - optfeature "nhmmer" >=sci-biology/hmmer-3.1 + optfeature "nhmmer" \>=sci-biology/hmmer-3.1 einfo "abblast/wublast from http://blast.advbiocomp.com/licensing" einfo "repeatmasker-libraries-20160829 (RepBase 21.12) is the last" einfo "version compatible with <repeatmasker-4.0.7" diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild similarity index 94% copy from sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild copy to sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild index 2ff6c8be6..9b4af2312 100644 --- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild +++ b/sci-biology/repeatmasker/repeatmasker-4.0.8-r1.ebuild @@ -20,7 +20,7 @@ DEPEND=">=dev-lang/perl-5.8" RDEPEND=" dev-perl/Text-Soundex sci-biology/phrap - <=sci-biology/repeatmasker-libraries-20160829 + >sci-biology/repeatmasker-libraries-20160829 sci-biology/rmblast !sci-biology/trf >=sci-biology/trf-bin-4.0.4 @@ -92,7 +92,7 @@ src_install() { doins -r util Matrices Libraries *.help keepdir /usr/share/${PN}/Libraries - dodoc README INSTALL *.help + dodoc README.md INSTALL *.help } pkg_postinst(){ @@ -104,8 +104,8 @@ pkg_postinst(){ einfo "Supported search engines are:" optfeature "cross_match" sci-biology/phrap optfeature "rmblast" sci-biology/rmblast - optfeature "nhmmer" >=sci-biology/hmmer-3.1 + 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 "repeatmasker-libraries-20160829 (RepBase 21.12) was the last" einfo "version compatible with <repeatmasker-4.0.7" }