1aa2bfd8c15486f23f6efeec5f4358f366cfad53
hiram
  Wed Dec 29 12:45:41 2021 -0800
updated scripts to tolerate database assemblies in the listings no redmine

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index c09c5ae..cfd3b40 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -42,30 +42,34 @@
     printf STDERR "duplicate name: '%s'\n", $commonName;
     exit 255;
   }
   $commonName{$asmId} = $commonName;
   push @orderList, $asmId;
   ++$assemblyCount;
 }
 close (FH);
 
 my $destDir = "/hive/data/genomes/asmHubs";
 
 my $buildDone = 0;
 my $orderIndex = 0;
 foreach my $asmId (@orderList) {
   ++$orderIndex;
+  if ($asmId !~ m/^GC/) {
+    printf STDERR "# not an assembly hub: %s\n", $asmId;
+    next;
+  }
   my ($gcPrefix, $accession, undef) = split('_', $asmId);
   my $accessionId = sprintf("%s_%s", $gcPrefix, $accession);
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
   $destDir = "/hive/data/genomes/asmHubs/$accessionDir/$accessionId";
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
   if ($gcPrefix eq "GCA") {
      $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId";
   }
   my $trackDb = "$buildDir/$asmId.trackDb.txt";
   if ( ! -s "${trackDb}" ) {
     printf STDERR "# %03d not built yet: %s\n", $orderIndex, $asmId;
     printf STDERR "# missing tdb: '%s'\n", $trackDb;