src/hg/utils/automation/doWindowMasker.pl 1.7

Index: src/hg/utils/automation/doWindowMasker.pl
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/automation/doWindowMasker.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 4 -r1.6 -r1.7
--- src/hg/utils/automation/doWindowMasker.pl	13 Aug 2007 20:45:19 -0000	1.6
+++ src/hg/utils/automation/doWindowMasker.pl	7 Mar 2009 00:06:33 -0000	1.7
@@ -34,9 +34,9 @@
 
 # Option defaults:
 my $defaultWorkhorse = 'least loaded';
 my $dbHost = 'hgwdev';
-my $unmaskedSeq = "$HgAutomate::clusterData/\$db/\$db.unmasked.2bit";
+my $unmaskedSeq = "$HgAutomate::hiveDataGenomes/\$db/\$db.unmasked.2bit";
 
 my $base = $0;
 $base =~ s/^(.*\/)?//;
 
@@ -50,9 +50,9 @@
 ";
   print STDERR $stepper->getOptionHelp();
   print STDERR <<_EOF_
     -buildDir dir         Use dir instead of default
-                          $HgAutomate::clusterData/\$db/$HgAutomate::trackBuild/WindowMasker.\$date
+                          $HgAutomate::hiveDataGenomes/\$db/$HgAutomate::trackBuild/WindowMasker.\$date
                           (necessary when continuing at a later date).
 _EOF_
   ;
   print STDERR &HgAutomate::getCommonOptionHelp('dbHost' => $dbHost,
@@ -64,14 +64,14 @@
     sdust: Another pass of WindowMasker using -sdust true.
     twobit: Make masked twobit files.
     cleanup: Removes or compresses intermediate files.
 All operations are performed in the build directory which is
-$HgAutomate::clusterData/\$db/$HgAutomate::trackBuild/WindowMasker.\$date unless -buildDir is given.
+$HgAutomate::hiveDataGenomes/\$db/$HgAutomate::trackBuild/WindowMasker.\$date unless -buildDir is given.
 ";
   # Detailed help (-help):
   print STDERR "
 Assumptions:
-1. $HgAutomate::clusterData/\$db/\$db.unmasked.2bit contains sequence for
+1. $HgAutomate::hiveDataGenomes/\$db/\$db.unmasked.2bit contains sequence for
    database/assembly \$db.  (This can be overridden with -unmaskedSeq.)
 " if ($detailed);
   print "\n";
   exit $status;
@@ -251,11 +251,11 @@
 # Establish what directory we will work in.
 my $date = `date +%Y-%m-%d`;
 chomp $date;
 $buildDir = $opt_buildDir ? $opt_buildDir :
-  "$HgAutomate::clusterData/$db/$HgAutomate::trackBuild/WindowMasker.$date";
+  "$HgAutomate::hiveDataGenomes/$db/$HgAutomate::trackBuild/WindowMasker.$date";
 $unmaskedSeq = $opt_unmaskedSeq ? $opt_unmaskedSeq :
-  "$HgAutomate::clusterData/$db/$db.unmasked.2bit";
+  "$HgAutomate::hiveDataGenomes/$db/$db.unmasked.2bit";
 
 # Do everything.
 $stepper->execute();