8fcf6d7d3fd31a5f0ff9d1793ab00eec67c7b04d
hiram
  Mon Sep 12 22:12:21 2022 -0700
now working thru gc5Base refs #29811

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index c663322..7e09fe6 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1105,65 +1105,65 @@
 _EOF_
   );
   $bossScript->execute();
 } # gatewayPage
 
 #########################################################################
 # * step: cytoBand [workhorse]
 sub doCytoBand {
   my $runDir = "$buildDir/trackData/cytoBand";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct cytoBand track and navigation ideogram";
   my $bossScript = newBash HgRemoteScript("$runDir/doCytoBand.bash",
                     $workhorse, $runDir, $whatItDoes);
 
-  if ( ! -s "$buildDir/$asmId.chrom.sizes" ) {
+  if ( ! -s "$buildDir/$defaultName.chrom.sizes" ) {
       printf STDERR "ERROR: sequence step not completed\n";
-      printf STDERR "can not find: $buildDir/$asmId.chrom.sizes\n";
+      printf STDERR "can not find: $buildDir/$defaultName.chrom.sizes\n";
       exit 255;
   }
 
   $bossScript->add(<<_EOF_
-export asmId=$asmId
+export asmId=$defaultName
 
 if [ ../../\$asmId.chrom.sizes -nt \$asmId.cytoBand.bb ]; then
   awk '{printf "%s\\t0\\t%d\\t\\tgneg\\n", \$1, \$2}' ../../\$asmId.chrom.sizes | sort -k1,1 -k2,2n > \$asmId.cytoBand.bed
   bedToBigBed -type=bed4+1 -as=\$HOME/kent/src/hg/lib/cytoBand.as -tab \$asmId.cytoBand.bed ../../\$asmId.chrom.sizes \$asmId.cytoBand.bb
 
   touch -r ../../\$asmId.chrom.sizes \$asmId.cytoBand.bb
 else
   printf "# cytoBand step previously completed\\n" 1>&2
   exit 0
 fi
 _EOF_
   );
   $bossScript->execute();
 } # cytoBand
 
 #########################################################################
 # * step: gc5Base [workhorse]
 sub doGc5Base {
   my $runDir = "$buildDir/trackData/gc5Base";
   &HgAutomate::mustMkdir($runDir);
 
   my $whatItDoes = "construct gc5Base bigWig track data";
   my $bossScript = newBash HgRemoteScript("$runDir/doGc5Base.bash",
                     $workhorse, $runDir, $whatItDoes);
 
   $bossScript->add(<<_EOF_
-export asmId=$asmId
+export asmId=$defaultName
 
 if [ ../../\$asmId.2bit -nt \$asmId.gc5Base.bw ]; then
   hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\
     ../../\$asmId.2bit \\
       | gzip -c > \$asmId.wigVarStep.gz
   wigToBigWig \$asmId.wigVarStep.gz ../../\$asmId.chrom.sizes \$asmId.gc5Base.bw
   rm -f \$asmId.wigVarStep.gz
   touch -r ../../\$asmId.2bit \$asmId.gc5Base.bw
 else
   printf "# gc5Base step previously completed\\n" 1>&2
   exit 0
 fi
 _EOF_
   );
   $bossScript->execute();