92509db0231e9b1ae83aa0c85182883dd8eabc9b
hiram
  Wed Sep 14 13:59:35 2022 -0700
fixup chainNet trackDb and now sending files to dynablat and arranging hub files to place it in use refs #29811

diff --git src/hg/utils/automation/asmHubChainNetTrackDb.pl src/hg/utils/automation/asmHubChainNetTrackDb.pl
index b824c72..6a19109 100755
--- src/hg/utils/automation/asmHubChainNetTrackDb.pl
+++ src/hg/utils/automation/asmHubChainNetTrackDb.pl
@@ -182,99 +182,104 @@
     track %sMafNetViewnet
     shortLabel Nets
     view net
     visibility dense
     subTrack %sChainNet
 ", $targetDb, $targetDb;
 
 $N = 0;
 $chainNetPriority = 1;
 foreach my $queryDb (@queryList) {
   my @targetAccession = split('_', $targetDb);
   my $targetAcc = sprintf("%s_%s", $targetAccession[0], $targetAccession[1]);
   my $QueryDb = ucfirst($queryDb);
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.net.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.net.summary.bb`;
+  if ( -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb) {
+printf STDERR "constructing net.bb links\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.bb  $buildDir/bbi/$targetDb.${queryDb}.net.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.net.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.net.summary.bb`;
   my $queryDate = "some date";
   my $queryAsmName = "";
   if ( $queryDb !~ m/^GC/ ) {
     $queryDate = `hgsql -N -e 'select description from dbDb where name="$queryDb"' hgcentraltest | sed -e 's/ (.*//;'`;
     chomp $queryDate;
   } else {
     ($queryDate, $queryAsmName) = &HgAutomate::hubDateName($queryDb);
   }
     printf "
         track net%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s mafNet
         longLabel %s%s (%s) mafNet Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.net.bb
         summary bbi/%s.%s.net.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
+  }
 
-  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb" ) {
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.synNet.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.synNet.summary.bb`;
+  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb" ) {
+printf STDERR "constructing synNet.bb links\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.bb  $buildDir/bbi/$targetDb.${queryDb}.synNet.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.synNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.synNet.summary.bb`;
     printf "
         track synNet%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s synNet
         longLabel %s%s (%s) Syntenic Net Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.synNet.bb
         summary bbi/%s.%s.synNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
 
   }
 
-  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb" ) {
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.rbestNet.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.rbestNet.summary.bb`;
+  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb" ) {
+printf STDERR "constructing rbestNet.bb links\n";
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.bb  $buildDir/bbi/$targetDb.${queryDb}.rbestNet.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.rbestNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.rbestNet.summary.bb`;
     printf "
         track rbestNet%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s rbestNet
         longLabel %s%s (%s) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.rbestNet.bb
         summary bbi/%s.%s.rbestNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;
 
   }
 
-  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb" ) {
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.bb`;
   `rm -f $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.summary.bb`;
+  if ( -s "$buildDir/trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb" ) {
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.bb  $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.bb`;
   `ln -s ../trackData/lastz.$queryDb/bigMaf/${targetAcc}.${queryDb}.liftOverNet.summary.bb  $buildDir/bbi/$targetDb.${queryDb}.liftOverNet.summary.bb`;
     printf "
         track liftOverNet%s
         parent %sMafNetViewnet
         subGroups view=net species=s%03d clade=c00
         shortLabel %s liftOverNet
         longLabel %s%s (%s) Lift Over Net Alignment
         type bigMaf
         bigDataUrl bbi/%s.%s.liftOverNet.bb
         summary bbi/%s.%s.liftOverNet.summary.bb
         speciesOrder %s
         html html/%s.chainNet
         priority %d
 ", $QueryDb, $targetDb, $N, $queryDb, $queryDb, $queryAsmName, $queryDate, $targetDb, $queryDb, $targetDb, $queryDb, $queryDb, $targetDb, $chainNetPriority++;