a02fe4b3289da1d30d52ba60b769644e9a3d8454
hiram
  Thu Oct 30 12:51:55 2025 -0700
correct start up for the bedResult step

diff --git src/hg/utils/automation/doLongdust.pl src/hg/utils/automation/doLongdust.pl
index bf407430769..d6867af7c61 100755
--- src/hg/utils/automation/doLongdust.pl
+++ src/hg/utils/automation/doLongdust.pl
@@ -91,40 +91,40 @@
   HgAutomate::processCommonOptions();
   my $err = $stepper->processOptions();
   usage(1) if ($err);
   $dbHost = $opt_dbHost if ($opt_dbHost);
 }
 
 #########################################################################
 # * step: setup [workhorse]
 sub doSetup {
   my $runDir = "$buildDir";
   if ( ! $opt_debug && (-s "$runDir/chrom.sizes" && -s "$runDir/part.list" )) {
      printf STDERR "# setup step already complete\n";
      return;
   }
   if (! $opt_debug) {
-    my @outs = ("$runDir/doSetup.bash",
+    my @outs = ("$runDir/setup.bash",
                 "$runDir/chrom.sizes",
                 "$runDir/part.list");
     HgAutomate::checkCleanSlate('setup', 'cluster', @outs);
   }
   HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "prepare files for longdust cluster run.";
   my $workhorse = $opt_debug ? "hgwdev" : HgAutomate::chooseWorkhorse();
-  my $bossScript = newBash HgRemoteScript("$runDir/doSetup.bash", $workhorse,
+  my $bossScript = newBash HgRemoteScript("$runDir/setup.bash", $workhorse,
 				      $runDir, $whatItDoes);
 
   my $tmpDir = HgAutomate::tmpDir();
   $bossScript->add(<<_EOF_
 rm -fr unmasked.2bit listFiles
 ln -s "$unmaskedSeq" unmasked.2bit
 
 twoBitInfo unmasked.2bit stdout | sort -k2nr > chrom.sizes
 
 export seqMax=`head -1 chrom.sizes | awk '{printf "%d", \$2+1}'`
 
 partitionSequence.pl -lstDir listFiles \$seqMax 0 \\
   unmasked.2bit chrom.sizes 10000
 ls -S listFiles/*.lst > part.list
 _EOF_
@@ -194,32 +194,31 @@
 _EOF_
   );
 
   $bossScript->execute() if (! $opt_debug);
 } # doCluster
 
 #########################################################################
 # * step: bedResult [fileServer]
 sub doBedResult {
   my $runDir = "$buildDir";
   if ( ! $opt_debug && -s "$runDir/longdust.bb") {
      printf STDERR "# bedResult step already complete\n";
      return;
   }
   my $whatItDoes = "Consolidate the cluster run bed.gz files.  Make single bed and bigBed file.";
-  HgAutomate::checkExistsUnlessDebug('cluster', 'cleanup', ("$runDir/longdust.bed.gz",
-           "$runDir/longdust.bb"));
+  HgAutomate::checkExistsUnlessDebug('cluster', 'cleanup', "$runDir/run.time");
   my $fileServer = $opt_debug ? "hgwdev" : HgAutomate::chooseFileServer($runDir);
   my $bossScript = newBash HgRemoteScript("$runDir/makeBed.bash", $fileServer,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_
 ls -S result/*.bed.gz | xargs zcat | gzip -c > longdust.bed.gz
 bedToBigBed -type=bed3 longdust.bed.gz chrom.sizes longdust.bb
 export totalBases=`ave -col=2 chrom.sizes | grep total | awk '{printf "%d", \$NF}'`
 export basesCovered=`bigBedInfo longdust.bb | grep basesCovered | awk '{printf "%s", \$NF}' | tr -d ','`
 export percentCovered=`echo \$basesCovered \$totalBases | awk '{printf "%.2f", 100*\$1/\$2}'`
 printf "%d bases of %d (%s%%) in intersection\n" "\$basesCovered" "\$totalBases" "\$percentCovered" > fb.longdust.txt
 cat fb.longdust.txt
 _EOF_
   );
   $bossScript->execute() if (! $opt_debug);
 } #doBedResult