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/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index aae2a7f..122303d 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -104,30 +104,31 @@
     printf STDERR "previous name: '%s'\n", $commonName{$asmId};
     printf STDERR "duplicate name: '%s'\n", $commonName;
     exit 255;
   }
   $commonName{$asmId} = $commonName;
   push @orderList, $asmId;
   printf STDERR "orderList[$assemblyCount] = $asmId\n";
   ++$assemblyCount;
 }
 close (FH);
 
 my $buildDone = 0;
 my $orderKey = 0;
 foreach my $asmId (@orderList) {
   ++$orderKey;
+  next if ($asmId !~ m/^GC/);
   my ($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);
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
   my $destDir = "/hive/data/genomes/asmHubs/$accessionDir/$accessionId";
   if ($gcPrefix eq "GCA") {
      $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId";
   }
   if ( ! -s "${buildDir}/${asmId}.chrom.sizes" ) {
     printf STDERR "# ERROR: missing ${asmId}.chrom.sizes in\n# ${buildDir}\n";
     next;
   }