257a178f6045d49ab8051fc298a2d021bec6790b
hiram
  Tue Apr 5 11:13:21 2022 -0700
adding liftOver tracks changing organism name adding otherAligners directory and fasta.fa.gz download refs #29207

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index f54362f..0bb2b53 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -21,68 +21,94 @@
 }
 
 my $downloadHost = "hgwdev";
 my @blatHosts = qw( dynablat-01 dynablat-01 );
 my @blatPorts = qw( 4040 4040 );
 my $blatHostDomain = ".soe.ucsc.edu";
 my $groupsTxt = `cat ~/kent/src/hg/makeDb/doc/asmHubs/groups.txt`;
 
 ################### writing out hub.txt file, twice ##########################
 sub singleFileHub($$$$$$$$$$$) {
   my ($fh1, $fh2, $accessionId, $orgName, $descr, $asmId, $defPos, $taxId, $trackDb, $accessionDir, $buildDir) = @_;
   my @fhN;
   push @fhN, $fh1;
   push @fhN, $fh2;
 
+  my %liftOverChain;	# key is 'otherDb' name, value is bbi path
+  my %liftOverGz;	# key is 'otherDb' name, value is lift.over.gz file path
+  my $hasChainNets = `ls -d $buildDir/trackData/lastz.* 2> /dev/null | wc -l`;
+  chomp $hasChainNets;
+  if ($hasChainNets) {
+    printf STDERR "# hasChainNets: %d\t%s\n", $hasChainNets, $asmId;
+    open (CH, "ls -d $buildDir/trackData/lastz.*|") or die "can not ls -d $buildDir/trackData/lastz.*";
+    while (my $line = <CH>) {
+      chomp $line;
+      my $otherDb = basename($line);
+      $otherDb =~ s/lastz.//;
+      my $OtherDb = ucfirst($otherDb);
+      my $bbiPath = "$buildDir/bbi/${asmId}.chainLiftOver${OtherDb}.bb";
+      if (-s "${bbiPath}") {
+        $liftOverChain{$otherDb} = "bbi/${asmId}.chainLiftOver${OtherDb}.bb";
+      }
+     my $loPath = "$buildDir/liftOver/${accessionId}To${OtherDb}.over.chain.gz";
+      if (-s "${loPath}") {
+    $liftOverGz{$otherDb} = "liftOver/${accessionId}To${OtherDb}.over.chain.gz";
+      }
+    }
+    close (CH);
+  }
   my $fileCount = 0;
   my @tdbLines;
   open (TD, "<$trackDb") or die "can not read trackDb: $trackDb";
   while (my $tdbLine = <TD>) {
      chomp $tdbLine;
      push @tdbLines, $tdbLine;
   }
   close (TD);
   foreach my $fh (@fhN) {
     printf $fh "hub %s genome assembly\n", $accessionId;
     printf $fh "shortLabel %s\n", $orgName;
     printf $fh "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId;
     printf $fh "useOneFile on\n";
     printf $fh "email hclawson\@ucsc.edu\n";
     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 "twoBitBptUrl %s.2bit.bpt\n", $accessionId;
     printf $fh "chromSizes %s.chrom.sizes.txt\n", $accessionId;
-    if ( -s "${buildDir}/${asmId}.chromAlias.bb" ) {
+    if ( (0 == 1) && -s "${buildDir}/${asmId}.chromAlias.bb" ) {
       printf $fh "chromAliasBb %s.chromAlias.bb\n", $accessionId;
     } else {
       printf $fh "chromAlias %s.chromAlias.txt\n", $accessionId;
     }
-    printf $fh "organism %s\n", $descr;
+    printf $fh "organism %s\n", $orgName;
     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 %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];
     }
+    foreach my $otherDb (sort keys %liftOverGz) {
+       printf $fh "liftOver.%s %s\n", $otherDb, $liftOverGz{$otherDb};
+    }
     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;
 my $inputList = shift;
@@ -173,31 +199,31 @@
   printf "taxId %s\n", $taxId if (length($taxId) > 1);
   printf "trackDb ../%s/%s/trackDb.txt\n", $accessionDir, $accessionId;
   printf "groups groups.txt\n";
   printf "description %s\n", $orgName;
   printf "twoBitPath ../%s/%s/%s.2bit\n", $accessionDir, $accessionId, $accessionId;
   printf "twoBitBptUrl ../%s/%s/%s.2bit.bpt\n", $accessionDir, $accessionId, $accessionId;
   printf "chromSizes ../%s/%s/%s.chrom.sizes.txt\n", $accessionDir, $accessionId, $accessionId;
 
   # wait until code gets out for v429 release before using chromAlias.bb
   # for the chromInfoPage display of hgTracks
   if ( (0 == 1) &&  -s "${buildDir}/${asmId}.chromAlias.bb" ) {
     printf "chromAliasBb ../%s/%s/%s.chromAlias.bb\n", $accessionDir, $accessionId, $accessionId;
   } else {
     printf "chromAlias ../%s/%s/%s.chromAlias.txt\n", $accessionDir, $accessionId, $accessionId;
   }
-  printf "organism %s\n", $descr;
+  printf "organism %s\n", $orgName;
   my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`;
   chomp $chrName;
   my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`;
   chomp $bigChrom;
   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", $descr;
@@ -230,36 +256,36 @@
   open (HT, ">$localHubTxt") or die "can not write to $localHubTxt";
 
   singleFileHub(\*HT, \*DL, $accessionId, $orgName, $descr, $asmId,
 	$defPos, $taxId, $trackDb, $accessionDir, $buildDir);
 
   my $localGenomesFile = "$buildDir/${asmId}.genomes.txt";
   open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
   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 "twoBitBptUrl %s.2bit.bpt\n", $accessionId;
   printf GF "chromSizes %s.chrom.sizes.txt\n", $accessionId;
-  if ( -s "${buildDir}/${asmId}.chromAlias.bb" ) {
+  if ( (0 == 1) && -s "${buildDir}/${asmId}.chromAlias.bb" ) {
     printf GF "chromAliasBb %s.chromAlias.bb\n", $accessionId;
   } else {
     printf GF "chromAlias %s.chromAlias.txt\n", $accessionId;
   }
-  printf GF "organism %s\n", $descr;
+  printf GF "organism %s\n", $orgName;
   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 $blatHost$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";