diff options
Diffstat (limited to 'sci-biology/repeatmasker/files')
-rw-r--r-- | sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch | 122 | ||||
-rw-r--r-- | sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch (renamed from sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch) | 0 |
2 files changed, 0 insertions, 122 deletions
diff --git a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch deleted file mode 100644 index 0b8a75c67..000000000 --- a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch +++ /dev/null @@ -1,122 +0,0 @@ ---- 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/files/RepeatMasker-open-4-0-6__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch index e4042190f..e4042190f 100644 --- a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch +++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch |