Index: src/hg/utils/automation/makeDownloads.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/makeDownloads.pl,v
retrieving revision 1.18
retrieving revision 1.19
diff -b -B -U 4 -r1.18 -r1.19
--- src/hg/utils/automation/makeDownloads.pl	2 Dec 2008 17:36:44 -0000	1.18
+++ src/hg/utils/automation/makeDownloads.pl	3 Mar 2009 21:46:55 -0000	1.19
@@ -16,8 +16,11 @@
 
 # Option variable names:
 use vars @HgAutomate::commonOptionVars;
 use vars @HgStepManager::optionVars;
+use vars qw/
+    $opt_ignoreRepeatMasker
+    /;
 
 # Specify the steps supported with -continue / -stop:
 my $stepper = new HgStepManager(
     [ { name => 'compress', func => \&doCompress },
@@ -44,8 +48,9 @@
 ";
   print STDERR $stepper->getOptionHelp();
   print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
 					'workhorse' => $defaultWorkhorse);
+  print STDERR "    -ignoreRepeatMasker   do not look for RM .out files\n";
   print STDERR "
 Automates generation of assembly download files for genome database \$db:
     compress: Create compressed download files, md5sum.txt and README.txt in
               $HgAutomate::clusterData/\$db/goldenPath/*/
@@ -77,8 +82,9 @@
 
 sub checkOptions {
   # Make sure command line options are valid/supported.
   my $ok = GetOptions(@HgStepManager::optionSpec,
+		      'ignoreRepeatMasker',
 		      @HgAutomate::commonOptionSpec,
 		      );
   &usage(1) if (!$ok);
   &usage(0, 1) if ($opt_help);
@@ -146,10 +152,14 @@
       } elsif ($chr eq 'chrM') {
 	# It is OK to lack RepeatMasker output for chrM too.
 	$rmFudge++;
       } else {
+	if (!$opt_ignoreRepeatMasker) {
 	warn "Missing RepeatMasker $outFile\n";
 	$problems++;
+	} else {
+	    $rmFudge++;
+	}
       }
       if (-e "$trfRunDir/$trfFile") {
 	push @chromTrfFiles, $trfFile;
       } elsif ($trfFile =~ /chrM\.bed$/) {
@@ -183,11 +193,22 @@
 # soft- and hard-masked .fa:
 cd $topDir
 
 tar cvzf $runDir/bigZips/chromAgp.tar.gz @chromAgpFiles
+_EOF_
+  );
+
+if (! $opt_ignoreRepeatMasker) {
+  $bossScript->add(<<_EOF_
 
 tar cvzf $runDir/bigZips/chromOut.tar.gz @chromOutFiles
 
+_EOF_
+  );
+}
+
+  $bossScript->add(<<_EOF_
+
 cd $runDir/$chromGz
 tar cvzf $runDir/bigZips/chromFa.tar.gz *.fa
 
 tar cvzf $runDir/bigZips/chromFaMasked.tar.gz *.fa.masked

