[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/files/, sci-biology/repeatmasker/

[Martin Mokrejs]

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"
 }