50d655bec99c9e0a4f201ced82513d4c936af575
hiram
  Wed Mar 3 20:14:44 2021 -0800
now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index 758f564..729cdd3 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -60,57 +60,77 @@
   $accessionDir .= "/" . substr($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", $trackDb;
     next;
   }
   ++$buildDone;
-  printf STDERR "# %03d symlinks %s\n", $buildDone, $accessionId;
-  printf STDERR "%s\n", $buildDir;
-  printf STDERR "%s\n", $destDir;
+  printf STDERR "# %03d symlinks %s %s\n", $buildDone, $accessionId, $asmId;
+#  printf STDERR "%s\n", $buildDir;
+#  printf STDERR "%s\n", $destDir;
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
+  `rm -f "${destDir}/${accessionId}.untrans.gfidx"`;
+  `rm -f "${destDir}/${accessionId}.trans.gfidx"`;
   `rm -f "${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}/${accessionId}_assembly_report.txt"`;
   `rm -f "${destDir}/${accessionId}.userTrackDb.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
+  `rm -f "${destDir}/download.genomes.txt"`;
   `rm -f "${destDir}/hub.txt"`;
+  `rm -f "${destDir}/download.hub.txt"`;
   `rm -f "${destDir}/groups.txt"`;
   `ln -s "${buildDir}/bbi" "${destDir}/bbi"` if (-d "${buildDir}/bbi");
   `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"` if (-d "${buildDir}/ixIxx");
   `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}/${asmId}.2bit" "${destDir}/${accessionId}.2bit"` if (-s "${buildDir}/${asmId}.2bit");
+   if (-s "${buildDir}/${accessionId}.untrans.gfidx") {
+      if (-s "${buildDir}/${accessionId}.trans.gfidx") {
+        `rm -f "${buildDir}/${asmId}.untrans.gfidx"`;
+        `rm -f "${buildDir}/${asmId}.trans.gfidx"`;
+        `ln -s "${buildDir}/${accessionId}.untrans.gfidx" "${destDir}/${accessionId}.untrans.gfidx"`;
+        `ln -s "${buildDir}/${accessionId}.trans.gfidx" "${destDir}/${accessionId}.trans.gfidx"`;
+      }
+   }
   `ln -s "${buildDir}/${asmId}.agp.gz" "${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}/download/${asmId}_assembly_report.txt" "${destDir}/${accessionId}_assembly_report.txt"` if (-s "${buildDir}/${asmId}_assembly_report.txt");
+  # trackDb.txt still needed for use by top-level genomes.txt file
   `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/trackDb.txt"` if (-s "${buildDir}/${asmId}.trackDb.txt");
-  `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/genomes.txt"` if (-s "${buildDir}/${asmId}.genomes.txt");
+  # genomes.txt obsolete now with single file
+#   `ln -s "${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}.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}/${asmId}.groups.txt");
   `ln -s "${buildDir}/${asmId}.userTrackDb.txt" "${destDir}/${accessionId}.userTrackDb.txt"` if ( -s "${buildDir}/${asmId}.userTrackDb.txt");
 }