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commit: 88c83795fd0b56239cc79b4b2c24e1d459dc348a |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Tue Dec 1 00:29:23 2015 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Tue Dec 1 00:29:23 2015 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=88c83795 |
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|
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sci-biology/repeatmasker: rename and move the patch file; drop old patch for a previous version |
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|
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Package-Manager: portage-2.2.18 |
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|
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sci-biology/repeatmasker/ChangeLog | 7 ++ |
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.../files/RepeatMasker-open-4-0-1__configure.patch | 122 --------------------- |
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...e.patch => repeatmasker-4.0.6__configure.patch} | 0 |
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3 files changed, 7 insertions(+), 122 deletions(-) |
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|
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diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog |
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index c7fadb6..872aa83 100644 |
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--- a/sci-biology/repeatmasker/ChangeLog |
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+++ b/sci-biology/repeatmasker/ChangeLog |
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@@ -2,6 +2,13 @@ |
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# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 |
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# $Id$ |
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|
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+ 01 Dec 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +files/repeatmasker-4.0.6__configure.patch, |
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+ -files/RepeatMasker-open-4-0-1__configure.patch, |
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+ -files/RepeatMasker-open-4-0-6__configure.patch: |
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+ sci-biology/repeatmasker: rename and move the patch file; drop old patch for a |
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+ previous version |
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+ |
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24 Nov 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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repeatmasker-4.0.1-r1.ebuild: |
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sci-biology/repeatmasker: improve einfo message |
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|
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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 |
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deleted file mode 100644 |
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index 0b8a75c..0000000 |
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--- a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch |
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+++ /dev/null |
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@@ -1,122 +0,0 @@ |
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---- configure.ori 2013-02-21 02:32:30.000000000 +0100 |
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-+++ configure 2015-11-24 19:54:50.630202150 +0100 |
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-@@ -253,17 +253,16 @@ |
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- close INVERS; |
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- } |
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- else { |
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-- print "\nYour RepeatMasker installation is missing a library file.\n" |
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-+ die "\nYour RepeatMasker installation is missing a library file.\n" |
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- . "RepeatMasker requires a minimal set of library sequences to run\n" |
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- . "properly. Please check that all files were extracted from the\n" |
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- . "distribution before re-running the configure program.\n\n"; |
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-- exit; |
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- } |
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- |
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- print "\n -- Building monolithic RM database..."; |
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- system( |
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- "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null" |
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--); |
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-+) and die "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!"; |
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- |
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- ## |
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- ## TRF location |
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-@@ -475,7 +474,7 @@ |
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- } |
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- close IN; |
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- close OUT; |
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-- system( "mv $configFile.tmp $configFile" ); |
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-+ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; |
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- } |
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- |
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- } |
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-@@ -607,15 +606,15 @@ |
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- } |
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- close IN; |
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- close OUT; |
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-- system( "mv $configFile.tmp $configFile" ); |
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-+ system( "mv $configFile.tmp $configFile" ) and die "Faled to mv $configFile.tmp $configFile: $!"; |
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- |
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- # Freeze RM and RMPep libraries for RepeatModeler use among others |
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- my $rmLocation = "$FindBin::Bin"; |
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- print "Building RMBlast frozen libraries..\n"; |
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- system( "$pgLocation/makeblastdb -dbtype nucl -in " |
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-- . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ); |
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-+ . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype nucl -in $rmLocation/Libraries/RepeatMasker.lib failed: $!"; |
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- system( "$pgLocation/makeblastdb -dbtype prot -in " |
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-- . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ); |
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-+ . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib failed with: $!"; |
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- |
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- my $pgDefault = &promptScreen( |
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- "", |
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-@@ -682,15 +681,15 @@ |
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- } |
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- close IN; |
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- close OUT; |
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-- system( "mv $configFile.tmp $configFile" ); |
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-+ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; |
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- |
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- # Freeze RM and RMPep libraries |
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- my $rmLocation = "$FindBin::Bin"; |
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- print "Building WUBlast/ABBlast frozen libraries..\n"; |
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- system( "$wuLocation/xdformat -n -I " |
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-- . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ); |
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-+ . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed with: $!"; |
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- system( "$wuLocation/xdformat -p -I " |
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-- . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ); |
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-+ . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with: $!"; |
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- |
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- my $wuDefault = &promptScreen( |
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- "", |
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-@@ -748,7 +747,7 @@ |
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- } |
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- } |
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- else { |
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-- print "ERROR: Could not find nhmmer program in this directory!\n"; |
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-+ print "ERROR: Could not find nhmmer program in '$location' directory!\n"; |
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- } |
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- if ( $goodParam == 0 ) { |
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- print "<PRESS ENTER TO CONTINUE>\n"; |
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-@@ -773,7 +772,7 @@ |
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- } |
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- close IN; |
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- close OUT; |
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-- system( "mv $configFile.tmp $configFile" ); |
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-+ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; |
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- |
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- my $default = &promptScreen( |
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- "", |
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-@@ -827,7 +826,7 @@ |
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- } |
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- close IN; |
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- close OUT; |
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-- system( "mv $configFile.tmp $configFile" ); |
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-+ system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!"; |
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- |
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- my $deDefault = &promptScreen( |
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- "", |
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-@@ -863,9 +862,6 @@ |
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- |
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- my $answer = undef; |
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- |
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-- # Clear the screen |
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-- system( "clear" ); |
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-- |
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- print "\n\n\n"; |
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- print $screenText; |
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- my $numLines = ( $screenText =~ s/(\n)/$1/g ); |
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---- configure.ori 2015-11-24 20:10:58.640204679 +0100 |
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-+++ configure 2015-11-24 20:11:00.970204685 +0100 |
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-@@ -728,11 +728,12 @@ |
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- # HMMER 3.0dev (March 2010); http://hmmer.org/ |
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- # HMMER 3.1dev_0.33 (July 2012); http://hmmer.org |
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- # HMMER hmmer3.1-snap20120830 (August 2012); http://hmmer.org/ |
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-+ # HMMER 3.1b2 (February 2015); http://hmmer.org/ |
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- while ( $result =~ /([^\n\r]*)[\n\r]/ig ) { |
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- my $line = $1; |
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- |
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- if ( $line =~ /^#\s+HMMER\s+(\d+\.\d+)((dev)?(_\d+\.\d+)?\s+\(.*\)).*/ |
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-- || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ ) |
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-+ || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ || $line =~ /^#\s+HMMER\s+(\d+\.\d+).*/) |
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- { |
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- if ( $1 >= 3.1 ) { |
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- $goodParam = 1; |
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|
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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 |
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similarity index 100% |
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rename from sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch |
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rename to sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch |