d79d3e1568e732852f341062f1604b7484572d8f
hiram
  Mon Dec 20 21:27:53 2021 -0800
now using fully qualified domain name to dynablat-01 refs #28654

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index a0465d9..aae2a7f 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -11,30 +11,31 @@
   printf STDERR "e.g.: mkGenomes.pl hgwdev 4040 vgp.primary.assemblies.tsv > .../vgp/download.genomes.txt\n";
   printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n";
   printf STDERR "\nthe two columns are 1: asmId (accessionId_assemblyName)\n";
   printf STDERR "column 2: common name for species, columns separated by tab\n";
   printf STDERR "result will write a local asmId.genomes.txt file for each hub\n";
   printf STDERR "and a local asmId.hub.txt file for each hub\n";
   printf STDERR "and a local asmId.groups.txt file for each hub\n";
   printf STDERR "and the output to stdout will be the overall genomes.txt\n";
   printf STDERR "index file for all genomes in the given list\n";
   exit 255;
 }
 
 my $downloadHost = "hgwdev";
 my @blatHosts = qw( dynablat-01 dynablat-01 );
 my @blatPorts = qw( 4040 4040 );
+my $blatHostDomain = ".soe.ucsc.edu";
 
 ################### writing out hub.txt file, twice ##########################
 sub singleFileHub($$$$$$$$$$) {
   my ($fh1, $fh2, $accessionId, $orgName, $descr, $asmId, $defPos, $taxId, $trackDb, $accessionDir) = @_;
   my @fhN;
   push @fhN, $fh1;
   push @fhN, $fh2;
 
   my $fileCount = 0;
   my @tdbLines;
   open (TD, "<$trackDb") or die "can not read trackDb: $trackDb";
   while (my $tdbLine = <TD>) {
      chomp $tdbLine;
      push @tdbLines, $tdbLine;
   }
@@ -48,33 +49,33 @@
     printf $fh "descriptionUrl html/%s.description.html\n", $asmId;
     printf $fh "\n";
     printf $fh "genome %s\n", $accessionId;
     printf $fh "taxId %s\n", $taxId if (length($taxId) > 1);
     printf $fh "groups groups.txt\n";
     printf $fh "description %s\n", $orgName;
     printf $fh "twoBitPath %s.2bit\n", $accessionId;
     printf $fh "chromSizes %s.chrom.sizes.txt\n", $accessionId;
     printf $fh "chromAlias %s.chromAlias.txt\n", $accessionId;
     printf $fh "organism %s\n", $descr;
     printf $fh "defaultPos %s\n", $defPos;
     printf $fh "scientificName %s\n", $descr;
     printf $fh "htmlPath html/%s.description.html\n", $asmId;
     # until blat server host is ready for hgdownload, avoid these lines
     if ($blatHosts[$fileCount] ne $downloadHost) {
-      printf $fh "blat %s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatPorts[$fileCount];
-      printf $fh "transBlat %s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatPorts[$fileCount];
-      printf $fh "isPcr %s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatPorts[$fileCount];
+      printf $fh "blat %s%s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatHostDomain, $blatPorts[$fileCount];
+      printf $fh "transBlat %s%s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatHostDomain, $blatPorts[$fileCount];
+      printf $fh "isPcr %s%s %s dynamic $accessionDir/$accessionId\n", $blatHosts[$fileCount], $blatHostDomain, $blatPorts[$fileCount];
     }
     printf $fh "\n";
     foreach my $tdbLine (@tdbLines) {
       printf $fh "%s\n", $tdbLine;
     }
     ++$fileCount;
   }
 }
 
 ##############################################################################
 my $home = $ENV{'HOME'};
 my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs";
 
 my $blatHost = shift;
 my $blatPort = shift;
@@ -173,33 +174,33 @@
   my $oneThird = int($bigChrom/3);
   my $tenK = $oneThird + 10000;
   $tenK = $bigChrom if ($tenK > $bigChrom);
   my $defPos="${chrName}:${oneThird}-${tenK}";
   if ( -s "$asmId/defaultPos.txt" ) {
     $defPos=`cat "$asmId/defaultPos.txt"`;
     chomp $defPos;
   }
   printf "defaultPos %s\n", $defPos;
   printf "orderKey %d\n", $buildDone;
   printf "scientificName %s\n", $descr;
   printf "htmlPath ../%s/%s/html/%s.description.html\n", $accessionDir, $accessionId, $asmId;
   # until blat server host is ready for hgdownload, avoid these lines
   if ($blatHost ne $downloadHost) {
     if ( -s "${destDir}/$accessionId.trans.gfidx" ) {
-      printf "blat $blatHost $blatPort dynamic $accessionDir/$accessionId\n";
-    printf "transBlat $blatHost $blatPort dynamic $accessionDir/$accessionId\n";
-      printf "isPcr $blatHost $blatPort dynamic $accessionDir/$accessionId\n";
+      printf "blat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
+    printf "transBlat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
+      printf "isPcr $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
     }
   }
   printf "\n";
 
   # the original multi-file system:
   my $localHubTxt = "$buildDir/${asmId}.hub.txt";
   open (HT, ">$localHubTxt") or die "can not write to $localHubTxt";
   printf HT "hub %s genome assembly\n", $accessionId;
   printf HT "shortLabel %s\n", $orgName;
   printf HT "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId;
   printf HT "genomesFile genomes.txt\n";
   printf HT "email hclawson\@ucsc.edu\n";
   printf HT "descriptionUrl html/%s.description.html\n", $asmId;
   close (HT);
 
@@ -217,33 +218,33 @@
   printf GF "genome %s\n", $accessionId;
   printf GF "taxId %s\n", $taxId if (length($taxId) > 1);
   printf GF "trackDb trackDb.txt\n";
   printf GF "groups groups.txt\n";
   printf GF "description %s\n", $orgName;
   printf GF "twoBitPath %s.2bit\n", $accessionId;
   printf GF "chromSizes %s.chrom.sizes.txt\n", $accessionId;
   printf GF "chromAlias %s.chromAlias.txt\n", $accessionId;
   printf GF "organism %s\n", $descr;
   printf GF "defaultPos %s\n", $defPos;
   printf GF "scientificName %s\n", $descr;
   printf GF "htmlPath html/%s.description.html\n", $asmId;
   # until blat server host is ready for hgdownload, avoid these lines
   if ($blatHost ne $downloadHost) {
     if ( -s "${destDir}/$accessionId.trans.gfidx" ) {
-      printf GF "blat $blatHost $blatPort dynamic $accessionDir/$accessionId\n";
-      printf GF "transBlat $blatHost $blatPort dynamic $accessionDir/$accessionId\n";
-     printf GF "isPcr $blatHost $blatPort dynamic $accessionDir/$accessionId\n";
+      printf GF "blat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
+      printf GF "transBlat $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
+     printf GF "isPcr $blatHost$blatHostDomain $blatPort dynamic $accessionDir/$accessionId\n";
     }
   }
   close (GF);
 
   my $localGroups = "$buildDir/${asmId}.groups.txt";
   open (GR, ">$localGroups") or die "can not write to $localGroups";
   print GR <<_EOF_
 name user
 label Custom Tracks
 priority 1
 defaultIsClosed 1
 
 name map
 label Mapping and Sequencing
 priority 2