a2c648a9f1539f12cfab4a5642b20e3550e9cd2e
hiram
  Fri Mar 25 13:54:35 2022 -0700
now using a bigBed file for chromAlias function refs #27228

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 7cdad79..18e47a6 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1916,34 +1916,38 @@
 # * step: trackDb [workhorse]
 sub doTrackDb {
   my $runDir = "$buildDir";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct asmId.trackDb.txt file";
   my $bossScript = newBash HgRemoteScript("$runDir/doTrackDb.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   if (! -s "${buildDir}/trackData/chromAlias/${asmId}.chromAlias.txt" ) {
     die "ERROR: can not find ${asmId}.chromAlias.txt in\n# ${buildDir}/trackData/chromAlias/\n";
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
+export buildDir=$buildDir
 
 rm -f \$asmId.chromAlias.txt
 ln -s trackData/chromAlias/\${asmId}.chromAlias.txt .
-\$HOME/kent/src/hg/utils/automation/asmHubTrackDb.sh \$asmId $runDir \\
+if [ -s trackData/chromAlias/\${asmId}.chromAlias.bb ]; then
+  ln -s -s trackData/chromAlias/\${asmId}.chromAlias.bb .
+fi
+\$HOME/kent/src/hg/utils/automation/asmHubTrackDb.sh \$asmId \$buildDir \\
    > \$asmId.trackDb.txt
 
 _EOF_
   );
   $bossScript->execute();
 } # trackDb
 
 #########################################################################
 # * step: cleanup [fileServer]
 sub doCleanup {
   my $runDir = "$buildDir";
   my $whatItDoes = "clean up or compresses intermediate files.";
   my $bossScript = newBash HgRemoteScript("$runDir/doCleanup.bash", $fileServer,
 				      $runDir, $whatItDoes);
   $bossScript->add(<<_EOF_