7580b50c5626bfbd3d6f90c7fb45dd899e335c64
hiram
  Mon Dec 9 13:00:46 2024 -0800
now staging everything on /gbdb/genark/ some redmine reference

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 43b191f..fe066ad 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -36,167 +36,214 @@
   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
+# top level global declaration for these three, 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
+#   for a set of backUp links for the dynamic blat machine,
+#   the gbdbDir is for the staging of the assembly hubs into /gbdb/
+#   to host the assembly hub in /gbdb/ instead of on hgdownload
 my $destDir = "/hive/data/genomes/asmHubs";
 my $dynaDir = "/hive/data/inside/dynaBlat/backUpLinks";
+my $gbdbDir = "/gbdb/genark";
 
 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";
+  $gbdbDir = "/gbdb/genark/$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 "${dynaDir}"`;
   }
+  if ( ! -d "${gbdbDir}" ) {
+    `mkdir -p "${gbdbDir}"`;
+  }
   `rm -f "${destDir}/bbi"`;
+  `rm -fr "${gbdbDir}/bbi"`;
   `rm -f "${destDir}/genes"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -f "${destDir}/genesGtf"`;
   `rm -f "${destDir}/liftOver"`;
+  `rm -f "${gbdbDir}/liftOver"`;
   `rm -f "${destDir}/otherAligners"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
+  `rm -fr "${gbdbDir}/html"`;
+  `rm -fr "${gbdbDir}/ixIxx"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
   `rm -f "${dynaDir}/${accessionId}.2bit"`;
+  `rm -f "${gbdbDir}/${accessionId}.2bit"`;
   `rm -f "${destDir}/${accessionId}.chrNames.2bit"`;
   `rm -f "${destDir}/${accessionId}.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.chrNames.fa.gz"`;
   `rm -f "${destDir}/${accessionId}.2bit.bpt"`;
+  `rm -f "${gbdbDir}/${accessionId}.2bit.bpt"`;
   `rm -f "${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}/${accessionId}.chrom.sizes.txt"`;
+  `rm -f "${gbdbDir}/${accessionId}.chrom.sizes.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.txt"`;
   `rm -f "${destDir}/${accessionId}.chromAlias.bb"`;
+  `rm -f "${gbdbDir}/${accessionId}.chromAlias.bb"`;
   `rm -f "${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}/${accessionId}.rmod.log.txt"`;
   `rm -f "${destDir}/${accessionId}.userTrackDb.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
   `rm -f "${destDir}/download.genomes.txt"`;
   `rm -f "${destDir}/hub.txt"`;
+  `rm -f "${gbdbDir}/hub.txt"`;
+  # it used to be standard practice to have a different hub.txt on genome-test
+  #   vs. the hub.txt on hgdownload.  They evolved into being identical, but
+  #   there may be a case in the future where this function may be required.
+  #   Also, the sendDownload script expects to use this download.hub.txt file.
   `rm -f "${destDir}/download.hub.txt"`;
   `rm -f "${destDir}/groups.txt"`;
-  `ln -s "${buildDir}/bbi" "${destDir}/bbi"` if (-d "${buildDir}/bbi");
+  `rm -f "${gbdbDir}/groups.txt"`;
+   if (-d "${buildDir}/bbi") {
+     `ln -s "${buildDir}/bbi" "${destDir}/bbi"`;
+     `ln -s "${buildDir}/bbi" "${gbdbDir}/bbi"`
+   }
   `ln -s "${buildDir}/genes" "${destDir}/genes"` if (-d "${buildDir}/genes");
-  `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"` if (-d "${buildDir}/ixIxx");
+   if (-d "${buildDir}/ixIxx") {
+     `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"`;
+     `ln -s "${buildDir}/ixIxx" "${gbdbDir}/ixIxx"`;
+   }
   `ln -s "${buildDir}/genesGtf" "${destDir}/genesGtf"` if (-d "${buildDir}/genesGtf");
-  `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"` if (-d "${buildDir}/liftOver");
+   if (-d "${buildDir}/liftOver") {
+      `ln -s "${buildDir}/liftOver" "${destDir}/liftOver"`;
+      `ln -s "${buildDir}/liftOver" "${gbdbDir}/liftOver"`;
+   }
   `ln -s "${buildDir}/otherAligners" "${destDir}/otherAligners"` if (-d "${buildDir}/otherAligners");
-  `ln -s ${buildDir}/html/*.html "${destDir}/html/"` if (-d "${buildDir}/html");
+   if (-d "${buildDir}/html") {
+     `ln -s ${buildDir}/html/*.html "${destDir}/html/"`;
+     `ln -s ${destDir}/html "${gbdbDir}/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/${asmId}/html/"`;
    if (-s "${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}/${accessionId}.2bit"`;
+     `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit" "${gbdbDir}/${accessionId}.2bit"`;
    }
    if (-s "${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}/${accessionId}.2bit.bpt"`;
+      `ln -s "${buildDir}/trackData/addMask/${asmId}.masked.2bit.bpt" "${gbdbDir}/${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}/${asmId}.chromAlias.bb");
+   if (-s "${buildDir}/${asmId}.chrom.sizes") {
+    `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/${accessionId}.chrom.sizes.txt"`;
+    `ln -s "${buildDir}/${asmId}.chrom.sizes" "${gbdbDir}/${accessionId}.chrom.sizes.txt"`;
+   }
+   if (-s "${buildDir}/${asmId}.chromAlias.txt") {
+    `ln -s "${buildDir}/${asmId}.chromAlias.txt" "${destDir}/${accessionId}.chromAlias.txt"`;
+   }
+   if (-s "${buildDir}/${asmId}.chromAlias.bb") {
+     `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${destDir}/${accessionId}.chromAlias.bb"`;
+     `ln -s "${buildDir}/${asmId}.chromAlias.bb" "${gbdbDir}/${accessionId}.chromAlias.bb"`;
+   }
    `ln -s "${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}/${asmId}.rmod.log.txt");
   `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/${accessionId}_assembly_report.txt"` if (-s "${buildDir}/download/${asmId}_assembly_report.txt");
   # trackDb.txt still needed for use by top-level genomes.txt file
   `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/trackDb.txt"` if (-s "${buildDir}/${asmId}.trackDb.txt");
   # genomes.txt obsolete now with single file
 #   `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/genomes.txt"` if (-s "${buildDir}/${asmId}.genomes.txt");
   `ln -s "${buildDir}/${asmId}.download.genomes.txt" "${destDir}/download.genomes.txt"` if (-s "${buildDir}/${asmId}.download.genomes.txt");
    if (-s "${buildDir}/${asmId}.singleFile.hub.txt") {
     `ln -s "${buildDir}/${asmId}.singleFile.hub.txt" "${destDir}/hub.txt"`;
+    `ln -s "${buildDir}/${asmId}.singleFile.hub.txt" "${gbdbDir}/hub.txt"`;
     `ln -s "${buildDir}/${asmId}.download.hub.txt" "${destDir}/download.hub.txt"` if (-s "${buildDir}/${asmId}.download.hub.txt");
    } else {
     `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/hub.txt"` if (-s "${buildDir}/${asmId}.hub.txt");
    }
-  `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/groups.txt"` if (-s "${buildDir}/${asmId}.groups.txt");
+   if (-s "${buildDir}/${asmId}.groups.txt") {
+      `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/groups.txt"`;
+      `ln -s "${buildDir}/${asmId}.groups.txt" "${gbdbDir}/groups.txt"`;
+   }
   `ln -s "${buildDir}/${asmId}.userTrackDb.txt" "${destDir}/${accessionId}.userTrackDb.txt"` if ( -s "${buildDir}/${asmId}.userTrackDb.txt");
    if (-s "${buildDir}/${asmId}.bigMaf.trackDb.txt") {
      `rm -f "${destDir}/${asmId}.bigMaf.trackDb.txt"`;
      `ln -s "${buildDir}/${asmId}.bigMaf.trackDb.txt" "${destDir}/${asmId}.bigMaf.trackDb.txt"`;
    }
 }