22a9ec8b34dd60a14257bdef408f21c03db601b4
hiram
  Mon Feb 17 16:06:38 2020 -0800
now using the shorter assembly name for genome identifier and fix some common names refs #23891

diff --git src/hg/makeDb/doc/asmHubs/mkSymLinks.pl src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
index a20691b..3564b72 100755
--- src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
+++ src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
@@ -45,42 +45,42 @@
 close (FH);
 
 my $destDir = "/hive/data/genomes/asmHubs";
 
 my $orderIndex = 0;
 foreach my $asmId (reverse(@orderList)) {
   ++$orderIndex;
   my ($gcPrefix, $accession, undef) = split('_', $asmId);
   my $accessionId = sprintf("%s_%s", $gcPrefix, $accession);
   printf STDERR "# %03d symlinks %s\n", $orderIndex, $accessionId;
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
 #  $accessionDir .= "/" . $asmId;
-  my $prevDestDir = "/hive/data/genomes/asmHubs/$accessionDir/$asmId";
+#  my $prevDestDir = "/hive/data/genomes/asmHubs/$accessionDir/$asmId";
   $destDir = "/hive/data/genomes/asmHubs/$accessionDir/$accessionId";
   my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
 #  printf STDERR "# working '${buildDir}' '${destDir}'\n";
 #  printf STDERR "# working '${buildDir}' '${prevDestDir}'\n";
   if ( ! -d "${destDir}" ) {
     `mkdir -p "${destDir}"`;
   }
-  if ( -d "${prevDestDir}" ) {
-    printf STDERR "# rm -fr '${prevDestDir}'\n";
-    `rm -fr "${prevDestDir}"`;
-  }
+#  if ( -d "${prevDestDir}" ) {
+#    printf STDERR "# rm -fr '${prevDestDir}'\n";
+#    `rm -fr "${prevDestDir}"`;
+#  }
   `rm -f "${destDir}/bbi"`;
   `rm -f "${destDir}/ixIxx"`;
   `rm -fr "${destDir}/html"`;
   `mkdir -p "${destDir}/html"`;
   `rm -f "${destDir}/${accessionId}.2bit"`;
   `rm -f "${destDir}/${accessionId}.agp.gz"`;
   `rm -f "${destDir}/${accessionId}.chrom.sizes"`;
   `rm -f "${destDir}/${accessionId}_assembly_report.txt"`;
   `rm -f "${destDir}/trackDb.txt"`;
   `rm -f "${destDir}/genomes.txt"`;
   `rm -f "${destDir}/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");