0104796f18e0ee85ccaa6f76caeacb055a42bc6c
hiram
  Mon Dec 9 12:09:08 2024 -0800
keep dynaBlat/backUpLinks hierarchy up to date refs #33526

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 6f83a4f..43b191f 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -36,79 +36,90 @@
   next if ($line =~ m/^#/);
   chomp $line;
   my ($asmId, $commonName) = split('\t', $line);
   if (defined($commonName{$asmId})) {
     printf STDERR "ERROR: duplicate asmId: '%s'\n", $asmId;
     printf STDERR "previous name: '%s'\n", $commonName{$asmId};
     printf STDERR "duplicate name: '%s'\n", $commonName;
     exit 255;
   }
   $commonName{$asmId} = $commonName;
   push @orderList, $asmId;
   ++$assemblyCount;
 }
 close (FH);
 
+# top level global declaration for these two, they will be specifically
+#   set later.  The destDir is for hgdownload staging, the dynaDir is
+#   for a set of backUp links for the dynamic blat machine
 my $destDir = "/hive/data/genomes/asmHubs";
+my $dynaDir = "/hive/data/inside/dynaBlat/backUpLinks";
 
 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";
+  $dynaDir = "/hive/data/inside/dynaBlat/backUpLinks/$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 "# error missing tdb: '%s'\n", $trackDb;
     next;
   }
   ++$buildDone;
   printf STDERR "# %03d symlinks %s %s\n", $buildDone, $asmId, $commonName{$asmId};
 #  printf STDERR "%s\n", $buildDir;
 #  printf STDERR "%s\n", $destDir;
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
+  if ( ! -d "${dynaDir}" ) {
+    `mkdir -p "${dynaDir}"`;
+  }
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/genes"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -f "${destDir}/genesGtf"`;
   `rm -f "${destDir}/liftOver"`;
   `rm -f "${destDir}/otherAligners"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
+  `rm -f "${dynaDir}/${accessionId}.2bit"`;
   `rm -f "${destDir}/${accessionId}.chrNames.2bit"`;
   `rm -f "${destDir}/${accessionId}.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.chrNames.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.2bit.bpt"`;
   `rm -f "${destDir}/${accessionId}.untrans.gfidx"`;
   `rm -f "${destDir}/${accessionId}.trans.gfidx"`;
+  `rm -f "${dynaDir}/${accessionId}.untrans.gfidx"`;
+  `rm -f "${dynaDir}/${accessionId}.trans.gfidx"`;
   `rm -f "${destDir}/${accessionId}.agp.gz"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.bb"`;
   `rm -f "${destDir}/${accessionId}_assembly_report.txt"`;
   `rm -f "${destDir}/${accessionId}.rmsk.customLib.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatMasker.out.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatMasker.version.txt"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.version.txt"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.families.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.families.stk.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.out.gz"`;
   `rm -f "${destDir}/${accessionId}.repeatModeler.2bit"`;
   `rm -f "${destDir}/${accessionId}.rmod.log.txt"`;
@@ -121,47 +132,52 @@
   `rm -f "${destDir}/groups.txt"`;
   `ln -s "${buildDir}/bbi" "${destDir}/bbi"` if (-d "${buildDir}/bbi");
   `ln -s "${buildDir}/genes" "${destDir}/genes"` if (-d "${buildDir}/genes");
   `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"` if (-d "${buildDir}/ixIxx");
   `ln -s "${buildDir}/genesGtf" "${destDir}/genesGtf"` if (-d "${buildDir}/genesGtf");
   `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"` if (-d "${buildDir}/liftOver");
   `ln -s "${buildDir}/otherAligners" "${destDir}/otherAligners"` if (-d "${buildDir}/otherAligners");
   `ln -s ${buildDir}/html/*.html "${destDir}/html/"` if (-d "${buildDir}/html");
    my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
    chomp $jpgFiles;
    if ($jpgFiles > 0) {
     `rm -f ${destDir}/html/*.jpg`;
     `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
    }
 #  `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
-  `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${destDir}/${accessionId}.2bit"` if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit");
+   if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit") {
+     `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${destDir}/${accessionId}.2bit"`;
+     `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${dynaDir}/${accessionId}.2bit"`;
+   }
    if (-s "${buildDir}/${asmId}.fa.gz") {
       `ln -s "${buildDir}/${asmId}.fa.gz" "${destDir}/${accessionId}.fa.gz"`;
    } else {
       printf STDERR "# error missing ${asmId}.fa.gz\n";
    }
   `ln -s "${buildDir}/${asmId}.chrNames.fa.gz" "${destDir}/${accessionId}.chrNames.fa.gz"` if (-s "${buildDir}/${asmId}.chrNames.fa.gz");
    if (-s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt") {
       `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt" "${destDir}/${accessionId}.2bit.bpt"`;
    } else {
       printf STDERR "# error missing ${asmId}.masked.2bit.bpt\n";
    }
   `ln -s "${buildDir}/${asmId}.chrNames.2bit" "${destDir}/${accessionId}.chrNames.2bit"` if (-s "${buildDir}/${asmId}.chrNames.2bit");
    if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
       if (-s "${buildDir}/${accessionId}.trans.gfidx") {
         `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
         `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
+        `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${dynaDir}/${accessionId}.untrans.gfidx"`;
+        `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${dynaDir}/${accessionId}.trans.gfidx"`;
       }
    }
   `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/${accessionId}.agp.gz"` if (-s "${buildDir}/${asmId}.agp.gz");
   `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes.txt"` if (-s "${buildDir}/${asmId}.chrom.sizes");
   `ln -s "${buildDir}/${asmId}.chromAlias.txt" "${destDir}/${accessionId}.chromAlias.txt"` if (-s "${buildDir}/${asmId}.chromAlias.txt");
   `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${destDir}/${accessionId}.chromAlias.bb"` if (-s "${buildDir}/${asmId}.chromAlias.bb");
    `ln -s "${buildDir}/${asmId}.rmsk.customLib.fa.gz" "${destDir}/${accessionId}.rmsk.customLib.fa.gz"` if (-s "${buildDir}/${asmId}.rmsk.customLib.fa.gz");
   `ln -s "${buildDir}/${asmId}.repeatMasker.out.gz" "${destDir}/${accessionId}.repeatMasker.out.gz"` if (-s "${buildDir}/${asmId}.repeatMasker.out.gz");
   `ln -s "${buildDir}/${asmId}.repeatModeler.out.gz" "${destDir}/${accessionId}.repeatModeler.out.gz"` if (-s "${buildDir}/${asmId}.repeatModeler.out.gz");
   `ln -s "${buildDir}/${asmId}.repeatMasker.version.txt" "${destDir}/${accessionId}.repeatMasker.version.txt"` if (-s "${buildDir}/${asmId}.repeatMasker.version.txt");
   `ln -s "${buildDir}/${asmId}.repeatModeler.version.txt" "${destDir}/${accessionId}.repeatModeler.version.txt"` if (-s "${buildDir}/${asmId}.repeatModeler.version.txt");
   `ln -s "${buildDir}/${asmId}.repeatModeler.families.fa.gz" "${destDir}/${accessionId}.repeatModeler.families.fa.gz"` if (-s "${buildDir}/${asmId}.repeatModeler.families.fa.gz");
   `ln -s "${buildDir}/${asmId}.repeatModeler.families.stk.gz" "${destDir}/${accessionId}.repeatModeler.families.stk.gz"` if (-s "${buildDir}/${asmId}.repeatModeler.families.stk.gz");
   `ln -s "${buildDir}/${asmId}.repeatModeler.2bit" "${destDir}/${accessionId}.repeatModeler.2bit"` if (-s "${buildDir}/${asmId}.repeatModeler.2bit");
   `ln -s "${buildDir}/${asmId}.rmod.log.txt" "${destDir}/${accessionId}.rmod.log.txt"` if (-s "${buildDir}/${asmId}.rmod.log.txt");