67d50873eca0ae6f595367077c9735b7d348e5c2
hiram
  Fri May 1 12:31:59 2020 -0700
adding functions to build VGP index pages refs #23734

diff --git src/hg/makeDb/doc/asmHubs/mkGenomes.pl src/hg/makeDb/doc/asmHubs/mkGenomes.pl
index 4ab17f0..f0fc827 100755
--- src/hg/makeDb/doc/asmHubs/mkGenomes.pl
+++ src/hg/makeDb/doc/asmHubs/mkGenomes.pl
@@ -34,72 +34,82 @@
 
 my @orderList;	# asmId of the assemblies in order from the *.list files
 # the order to read the different .list files:
 my $assemblyCount = 0;
 
 open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp $line;
   my ($commonName, $asmId) = split('\t', $line);
   push @orderList, $asmId;
   ++$assemblyCount;
 }
 close (FH);
 
-my $orderKey = 1;
+my $buildDone = 0;
+my $orderKey = 0;
 foreach my $asmId (reverse(@orderList)) {
+  ++$orderKey;
   my ($gcPrefix, $accession, undef) = split('_', $asmId);
   my $accessionId = sprintf("%s_%s", $gcPrefix, $accession);
   my $accessionDir = substr($asmId, 0 ,3);
   $accessionDir .= "/" . substr($asmId, 4 ,3);
   $accessionDir .= "/" . substr($asmId, 7 ,3);
   $accessionDir .= "/" . substr($asmId, 10 ,3);
-  my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/" . substr($asmId, 0 ,3);
-  $buildDir .= "/" . substr($asmId, 4 ,3);
-  $buildDir .= "/" . substr($asmId, 7 ,3);
-  $buildDir .= "/" . substr($asmId, 10 ,3);
-  $buildDir .= "/" . $asmId;
+  my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId";
+  if ($gcPrefix eq "GCA") {
+     $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId";
+  }
   my $asmReport="$buildDir/download/${asmId}_assembly_report.txt";
-  next if (! -s $asmReport);
-printf STDERR "# %03d genomes.txt %s/%s\n", $orderKey, $accessionDir, $accessionId;
+  my $trackDb = "$buildDir/$asmId.trackDb.txt";
+  if ( ! -s "${trackDb}" ) {
+    printf STDERR "# %03d not built yet: %s\n", $orderKey, $asmId;
+    next;
+  }
+  if ( ! -s "${asmReport}" ) {
+    printf STDERR "# %03d missing assembly_report: %s\n", $orderKey, $asmId;
+    next;
+  }
+  ++$buildDone;
+printf STDERR "# %03d genomes.txt %s/%s\n", $buildDone, $accessionDir, $accessionId;
   my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
   chomp $descr;
   my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`;
   chomp $orgName;
   $orgName = $betterName{$asmId} if (exists($betterName{$asmId}));
 
   printf "genome %s\n", $accessionId;
   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 "organism %s\n", $descr;
   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", $orderKey++;
+  printf "orderKey %d\n", $buildDone;
   printf "scientificName %s\n", $descr;
   printf "htmlPath ../%s/%s/html/%s.description.html\n", $accessionDir, $accessionId, $asmId;
   printf "\n";
   my $localGenomesFile = "$buildDir/${asmId}.genomes.txt";
   my $localOrderKey;
   open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
   printf GF "genome %s\n", $accessionId;
   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 "organism %s\n", $descr;
   printf GF "defaultPos %s\n", $defPos;
   printf GF "orderKey %d\n", $localOrderKey++;
   printf GF "scientificName %s\n", $descr;