bf0cbaeb5efbf31609492be27319a3237996d522
hiram
  Mon Apr 12 10:47:02 2021 -0700
now construction dynamic blat indexes refs #26658

diff --git src/hg/utils/automation/doAssemblyHub.pl src/hg/utils/automation/doAssemblyHub.pl
index 6295d3a..b6f4a00 100755
--- src/hg/utils/automation/doAssemblyHub.pl
+++ src/hg/utils/automation/doAssemblyHub.pl
@@ -1379,37 +1379,45 @@
                     $workhorse, $runDir, $whatItDoes);
 
   my $wmMasked=`grep "masked total" $buildDir/trackData/windowMasker/faSize.$asmId.cleanWMSdust.txt | awk '{print \$1}' | sed -e 's/%//;'`;
   my $rmMasked = 0;
   if (! $noRmsk) {
     $rmMasked=`grep "masked total" $buildDir/trackData/repeatMasker/faSize.rmsk.txt | awk '{print \$1}' | sed -e 's/%//;'`;
   }
 
   my $src2BitToMask = "../repeatMasker/$asmId.rmsk.2bit";
   if ($noRmsk || ($wmMasked > $rmMasked)) {
     $src2BitToMask = "../windowMasker/$asmId.cleanWMSdust.2bit";
   }
 
   $bossScript->add(<<_EOF_
 export asmId=$asmId
+export accessionId=`echo \$asmId | cut -d'_' -f1-2`
 
 if [ ../simpleRepeat/trfMask.bed.gz -nt \$asmId.masked.faSize.txt ]; then
   twoBitMask $src2BitToMask -type=.bed \\
      -add ../simpleRepeat/trfMask.bed.gz \$asmId.masked.2bit
   twoBitToFa \$asmId.masked.2bit stdout | faSize stdin > \$asmId.masked.faSize.txt
   touch -r \$asmId.masked.2bit \$asmId.masked.faSize.txt
   cp -p \$asmId.masked.faSize.txt ../../\$asmId.faSize.txt
+  ln \$asmId.masked.2bit \$accessionId.2bit
+  gfServer -trans index ../../\$accessionId.trans.gfidx \$accessionId.2bit &
+  gfServer -stepSize=5 index ../../\$accessionId.untrans.gfidx \$accessionId.2bit
+  wait
+  rm \$accessionId.2bit
+  touch -r \$asmId.masked.2bit ../../\$accessionId.trans.gfidx
+  touch -r \$asmId.masked.2bit ../../\$accessionId.untrans.gfidx
 else
   printf "# addMask step previously completed\\n" 1>&2
   exit 0
 fi
 _EOF_
   );
 
   $bossScript->execute();
 } # addMask
 
 #########################################################################
 # * step: windowMasker [workhorse]
 sub doWindowMasker {
   my $runDir = "$buildDir/trackData/windowMasker";