e3c90a0c1514cc8f4e0bf17618fd2d2d06e235ef
hiram
  Mon May 2 10:16:21 2022 -0700
clean up loose ends no redmine

diff --git src/hg/utils/automation/doXenoRefGene.pl src/hg/utils/automation/doXenoRefGene.pl
index ca80d0e..ac82f68 100755
--- src/hg/utils/automation/doXenoRefGene.pl
+++ src/hg/utils/automation/doXenoRefGene.pl
@@ -259,48 +259,48 @@
     | gnusort -S100G --parallel=32 -k10,10 > \$db.all.psl
 
 pslCDnaFilter -minId=0.35 -minCover=0.25  -globalNearBest=0.0100 -minQSize=20 \\
   -ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap \\
     \$db.all.psl \$db.xenoRefGene.psl
 
 pslCheck -targetSizes=\$db.chrom.sizes \\
   -querySizes=$mrnas/xenoRefMrna.sizes \\
      \$db.xenoRefGene.psl
 _EOF_
   );
   $bossScript->execute();
 } # doFilterPsl
 
 #########################################################################
-# * step: make gp [workhorse]
+# * step: make gp [dbHost]
 sub doMakeGp {
   my $runDir = $buildDir;
   &HgAutomate::mustMkdir($runDir);
 
   # First, make sure we're starting clean.
   if (! -e "$runDir/$db.xenoRefGene.psl") {
     die "doMakeGp: the previous step filterPsl did not complete \n" .
       "successfully ($buildDir/$db.xenoRefGene.psl does not exist).\nPlease " .
       "complete the previous step: -continue=filterPsl\n";
   } elsif (-e "$runDir/$db.xenoRefGene.bb" ) {
     die "doMakeGp: looks like this was run successfully already\n" .
       "($db.xenoRefGene.bb exists).  Either run with -continue cleanup\n" .
 	"or move aside/remove $runDir/$db.xenoRefGene.bb\nand run again.\n";
   }
 
   my $whatItDoes = "Makes bigGenePred.bb file from filterPsl output.";
-  my $bossScript = newBash HgRemoteScript("$runDir/makeGp.bash", $workhorse,
+  my $bossScript = newBash HgRemoteScript("$runDir/makeGp.bash", $dbHost,
 				      $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
 export db="$db"
 export buildDir="$buildDir"
 
 if [ -s "\$db.xenoRefGene.psl" ]; then
   grep NR_ \$db.xenoRefGene.psl > NR.psl
   grep NM_ \$db.xenoRefGene.psl > NM.psl
   mrnaToGene -cdsDb=hgFixed NM.psl NM.gp
   mrnaToGene -noCds NR.psl NR.gp
   cat NM.gp NR.gp | genePredSingleCover stdin \$db.xenoRefGene.gp
   genePredCheck -db=\$db -chromSizes=\$db.chrom.sizes \$db.xenoRefGene.gp
   genePredToBed \$db.xenoRefGene.gp stdout \\
     | bedToExons stdin stdout | bedSingleCover.pl stdin > \$db.exons.bed