6ddbb235ad633ecb2f7958329710b79fb07ff1c5
hiram
  Tue Sep 16 11:51:08 2025 -0700
adding the quickLift symlinks to /gbdb/ when database assembly refs #35575

diff --git src/hg/utils/automation/doBlastzChainNet.pl src/hg/utils/automation/doBlastzChainNet.pl
index 27298514d92..4cf99b901cb 100755
--- src/hg/utils/automation/doBlastzChainNet.pl
+++ src/hg/utils/automation/doBlastzChainNet.pl
@@ -1617,30 +1617,31 @@
   # Make sure previous stage was successful.
   my $successFile = "$runDir/$tDb.$qDb.all.chain.gz";
   if (! $isSelf && -s "$runDir/$tDb.$qDb.net.gz") {
      $successFile = "$runDir/$tDb.$qDb.net.gz";
   }
   if (! -e $successFile && ! $opt_debug) {
     die "installDownloads: looks like previous stage was not successful " .
       "(can't find $successFile).\n";
   }
   my $goldenPath = $HgAutomate::goldenPath;
   if ($tDb =~ m/^GC/) {
      $goldenPath = &HgAutomate::asmHubDownloadDir($tDb);
   }
   &dumpDownloadReadme("$runDir/README.txt");
   my $over = $tDb . "To$QDb.over.chain.gz";
+  my $quick = $qDb;
   my $liftOverDir = "$HgAutomate::clusterData/$tDb/$HgAutomate::trackBuild/liftOver";
   if ($tDb =~ m/^GC/) {
      $liftOverDir = &HgAutomate::asmHubBuildDir($tAsmId) . "/liftOver";
   }
   my $gpLiftOverDir = "$goldenPath/$tDb/liftOver";
   my $gbdbLiftOverDir = "$HgAutomate::gbdb/$tDb/liftOver";
   my $gbdbQuickLiftDir = "$HgAutomate::gbdb/$tDb/quickLift";
   my $andNets = $isSelf ? "." :
     ", nets and axtNet,\n" .
     "# and copies the liftOver chains to the liftOver download dir.";
   my $whatItDoes = "It creates the download directory for chains$andNets";
   my $bossScript = new HgRemoteScript("$runDir/installDownloads.csh", $dbHost,
 				      $runDir, $whatItDoes, $DEF);
   $bossScript->add(<<_EOF_
 mkdir -p $goldenPath/$tDb
@@ -1664,33 +1665,38 @@
       );
     }
     $bossScript->add(<<_EOF_
 
 $axt
 
 mkdir -p $gpLiftOverDir
 rm -f $gpLiftOverDir/$over
 ln -s $liftOverDir/$over $gpLiftOverDir/$over
 _EOF_
       );
     if ($tDb !~ m/^GC/) {
       $bossScript->add(<<_EOF_
 mkdir -p $gbdbLiftOverDir $gbdbQuickLiftDir
 rm -f $gbdbLiftOverDir/$over
+rm -f $gbdbQuickLiftDir/${quick}.bb
+rm -f $gbdbQuickLiftDir/${quick}.link.bb
+ln -s $buildDir/axtChain/$tDb.$qDb.quick.bb $gbdbQuickLiftDir/${quick}.bb
+ln -s $buildDir/axtChain/$tDb.$qDb.quickLink.bb $gbdbQuickLiftDir/${quick}.link.bb
 ln -s $liftOverDir/$over $gbdbLiftOverDir/$over
 hgAddLiftOverChain -minMatch=0.1 -multiple -path=$gbdbLiftOverDir/$over \\
   $tDb $qDb
+$ENV{'HOME'}/kent/src/hg/utils/automation/addQuickLift.py $tDb $qDb $gbdbQuickLiftDir/${quick}.bb
 _EOF_
       );
     }
 
     $bossScript->add(<<_EOF_
 unsetenv TMPDIR
 if ( -d "/data/tmp" ) then
   setenv TMPDIR "/data/tmp"
 else if ( -d "/scratch/tmp" ) then
   setenv TMPDIR "/scratch/tmp"
 else
   setenv TMPDIR "/tmp"
 endif
 # Update (or create) liftOver/md5sum.txt with the new .over.chain.gz.
 if (-e $gpLiftOverDir/md5sum.txt) then