c69c1e60152da91f9b2282ee3e3faa041309de80
hiram
  Tue Jun 24 15:32:45 2025 -0700
Eliminate gfidx indexes from downloads

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 48bd32e3b01..03d5c141b4f 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -340,36 +340,36 @@
   chomp $bigChrom;
   my $oneThird = int($bigChrom/3);
   my $tenK = $oneThird + 10000;
   $tenK = $bigChrom if ($tenK > $bigChrom);
   my $defPos="${chrName}:${oneThird}-${tenK}";
   if ( -s "$buildDir/defaultPos.txt" ) {
     $defPos=`cat "$buildDir/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}/$accessionId.trans.gfidx" ) {
+    if ( -s "${buildDir}/$accessionId.trans.gfidx" ) {
       printf "blat $blatHost$blatHostDomain %d dynamic $accessionDir/$accessionId\n", $blatPort + $hugeGenome;
     printf "transBlat $blatHost$blatHostDomain %d dynamic $accessionDir/$accessionId\n", $blatPort + $hugeGenome;
       printf "isPcr $blatHost$blatHostDomain %d dynamic $accessionDir/$accessionId\n", $blatPort + $hugeGenome;
     } else {
-      printf STDERR "# missing ${destDir}/$accessionId.trans.gfidx\n";
+      printf STDERR "# missing ${buildDir}/$accessionId.trans.gfidx\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 genome-www\@soe.ucsc.edu\n";
   printf HT "descriptionUrl html/%s.description.html\n", $asmId;
   close (HT);
 
@@ -395,31 +395,31 @@
   printf GF "chromSizes %s.chrom.sizes.txt\n", $accessionId;
   if ( -s "${buildDir}/${asmId}.chromAlias.bb" ) {
     printf GF "chromAliasBb %s.chromAlias.bb\n", $accessionId;
   } else {
     printf GF "chromAlias %s.chromAlias.txt\n", $accessionId;
   }
   if ($chromAuthority =~ m/^chromAuthority/) {
      printf GF "%s\n", $chromAuthority;
   }
   printf GF "organism %s %s\n", $assemblyName, $asmDate;
   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}/$accessionId.trans.gfidx" ) {
+    if ( -s "${buildDir}/$accessionId.trans.gfidx" ) {
       printf GF "blat $blatHost$blatHostDomain %d dynamic $accessionDir/$accessionId\n", $blatPort + $hugeGenome;
       printf GF "transBlat $blatHost$blatHostDomain %d dynamic $accessionDir/$accessionId\n", $blatPort + $hugeGenome;
      printf GF "isPcr $blatHost$blatHostDomain %d dynamic $accessionDir/$accessionId\n", $blatPort + $hugeGenome;
     }
   }
   close (GF);
 
   my $localGroups = "$buildDir/${asmId}.groups.txt";
   open (GR, ">$localGroups") or die "can not write to $localGroups";
   printf GR "%s", $groupsTxt;
   close (GR);
 }
 
 __END__