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|
--- configure.ori 2015-11-24 20:56:46.000000000 +0100
+++ configure 2015-11-24 20:59:58.000000000 +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 $wuDefault = &promptScreen(
"",
@@ -756,7 +755,7 @@
}
}
else {
- print "ERROR: Could not find nhmmer program in this directory!\n";
+ print "ERROR: Could not find nhmmer program in '$location' directory!\n";
}
}
@@ -776,7 +775,7 @@
}
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(
"",
@@ -830,7 +829,7 @@
}
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(
"",
@@ -866,9 +865,6 @@
my $answer = undef;
- # Clear the screen
- system( "clear" );
-
print "\n\n\n";
print $screenText;
my $numLines = ( $screenText =~ s/(\n)/$1/g );
|
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