2862b2a8ea3a56805265df693bf94a4ed7d07cca
hiram
  Thu Jul 21 18:04:51 2022 -0700
adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545

diff --git src/hg/makeDb/doc/asmHubs/commonHtml.pm src/hg/makeDb/doc/asmHubs/commonHtml.pm
index 82e6a5f..6be84f6 100644
--- src/hg/makeDb/doc/asmHubs/commonHtml.pm
+++ src/hg/makeDb/doc/asmHubs/commonHtml.pm
@@ -13,60 +13,62 @@
 # This is a listing of the public methods and variables (which should be
 # treated as constants) exported by this module:
 @EXPORT_OK = (
   qw( otherHubLinks htmlFooter )
 );
 
 # otherHubLinks: arg one: vgpIndex, arg two: asmHubName, arg three: orderList
 # arguments allow decision on customization of the table for different
 # types of assembly hubs
 
 sub otherHubLinks($$) {
 
   my ($vgpIndex, $asmHubName) = @_;
 
 my %asmCounts;	# key is hubName, value is number of assemblies
-my @hubList = qw(primates mammals birds fish vertebrate invertebrate plants fungi);
+my @hubList = qw(primates mammals birds fish vertebrate invertebrate plants fungi viral);
 foreach my $hubName (@hubList) {
   my $asmCount = `grep -v "^#" ../${hubName}AsmHub/${hubName}.orderList.tsv | wc -l`;
   chomp $asmCount;
   $asmCounts{$hubName} = $asmCount;
 }
 my $vgpCount = `grep -h -v "^#" ../vgpAsmHub/vgp.*.orderList.tsv | wc -l`;
 chomp $vgpCount;
 $asmCounts{'vgp'} = $vgpCount;
 my $legacyCount = `grep -h -v "^#" ../legacyAsmHub/legacy.orderList.tsv | wc -l`;
 chomp $legacyCount;
 $asmCounts{'legacy'} = $legacyCount;
 
 # different table output for VGP index
 
-if ((0 == $vgpIndex) && ($asmHubName ne "viral")) {
+if ((0 == $vgpIndex)) {
   printf "<p>\n<table border='1' style='margin-left:auto; margin-right:auto;'><thead>\n";
   printf "<tr><th colspan=4 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n";
   printf "<tr><th>Collection</th>\n";
   printf "    <th>Hub index pages:</th>\n";
   printf "    <th>Assembly statistics:</th>\n";
   printf "    <th>Track statistics:</th>\n";
   printf "</tr>\n";
   foreach my $hubName (@hubList) {
     if ($hubName =~ m/^vertebrate/) {
       printf "<tr><th>other vertebrates</th>\n";
     } elsif ($hubName =~ m/fish/) {
       printf "<tr><th>Fishes</th>\n";
     } elsif ($hubName =~ m/invertebrate/) {
       printf "<tr><th>Invertebrates</th>\n";
+    } elsif ($hubName =~ m/viral/) {
+      printf "<tr><th>Viruses</th>\n";
     } else {
       printf "<tr><th>%s</th>\n", ucfirst($hubName);
     }
     printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", $hubName, $asmCounts{$hubName};
     printf "    <th><a href='../%s/asmStats.html'>assembly stats</a></th>\n", $hubName;
     printf "    <th><a href='../%s/trackData.html'>track stats</a></th>\n", $hubName;
     printf "</tr>\n";
   }
   printf "<tr><th>VGP - Vertebrate Genome Project</th>\n";
   printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "VGP", $asmCounts{'vgp'};
   printf "    <th><a href='../VGP/asmStats.html'>assembly stats</a></th>\n";
   printf "    <th><a href='../VGP/trackData.html'>track stats</a></th>\n";
   printf "</tr>\n";
   printf "<tr><th>legacy/superseded</th>\n";
   printf "    <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "legacy", $asmCounts{'legacy'};