6d0decb929aff8d8b41c078b4ace21003ac3ec31
hiram
  Sat Apr 30 17:21:41 2022 -0700
fix broken row tag and add reference to assemblyRequest.html refs #29237

diff --git src/hg/makeDb/doc/asmHubs/hubIndex.pl src/hg/makeDb/doc/asmHubs/hubIndex.pl
index 4ed3494..2115fa2 100755
--- src/hg/makeDb/doc/asmHubs/hubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/hubIndex.pl
@@ -21,31 +21,30 @@
 <!--#include virtual="$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <h1>GenArk: UCSC Genome Archive</h1>
 
 '
 }
 
 #############################################################################
 sub endHtml() {
 printf '
 </div><!-- closing gbsPage from gbPageStartHardcoded.html -->
 </div><!-- closing container-fluid from gbPageStartHardcoded.html -->
 <!--#include virtual="$ROOT/inc/gbFooterHardcoded.html"-->
 <script type="text/javascript" src="<!--#echo var="ROOT" -->/js/sorttable.js"></script>
 <script type="text/javascript" src="<!--#echo var="ROOT" -->/js/analytics.js"></script>
-
 </body></html>
 '
 }
 
 #############################################################################
 startHtml;
 
 my %expectedList = (
  "VGP" => 1,
  "birds" => 1,
  "fish" => 1,
  "globalReference" => 1,
  "mammals" => 1,
  "primates" => 1,
  "vertebrate" => 1,
@@ -141,31 +140,31 @@
 my $genomeCount = `grep -h ^genome /mirrordata/hubs/VGP/*enomes.txt | wc -l`;
 chomp $genomeCount;
 $genomeCounts{"VGP"} = $genomeCount;
 
 my @checkList = ('primates', 'mammals', 'birds', 'fish', 'vertebrate', 'legacy', 'plants', "invertebrate", "fungi", 'globalReference');
 
 foreach my $hubSet (@checkList) {
   $genomeCount = `grep -h ^genome /mirrordata/hubs/$hubSet/genomes.txt | wc -l`;
   chomp $genomeCount;
   $genomeCounts{$hubSet} = $genomeCount;
 }
 
 my $hubCount = 0;
 
 printf "<table class='sortable' border='1'>\n";
-printf "<thead>\n";
+printf "<thead><tr>\n";
 printf "  <th>hub&nbsp;gateway</th>\n";
 printf "  <th>description</th>\n";
 printf "</tr></thead><tbody>\n";
 
 # construct table
 foreach my $orderUp (@orderOutHubs) {
   printf "<tr>\n";
   ++$hubCount;
   if ($orderUp eq "fish") {
      printf "    <td><a href='%s/%s' target=_blank>fishes</a></td>\n", $orderUp, $indexPage{$orderUp};
   } else {
      printf "    <td><a href='%s/%s' target=_blank>%s</a></td>\n", $orderUp, $indexPage{$orderUp}, $orderUp;
   }
   if (defined($genomeCounts{$orderUp})) {
     printf "    <td>%s (%d assemblies)</td>\n", $titles{$orderUp}, $genomeCounts{$orderUp};
@@ -175,16 +174,20 @@
   printf "</tr>\n";
 }
 
 printf "</tbody></table>\n";
 
 my $totalAsmHubs = `grep -v "^#" /mirrordata/hubs/UCSC_GI.assemblyHubList.txt | wc -l`;
 chomp $totalAsmHubs;
 printf "<p>\n";
 printf "Please note: text file <a href='UCSC_GI.assemblyHubList.txt' target=_blank>listing</a> of %d NCBI/VGP genome assembly hubs\n", $totalAsmHubs;
 printf "</p>\n";
 
 printf "<p>\n";
 printf "Please note, the <em>invertebrate</em> category contains more than just <em>invertebrate</em> animals.  Until these clades are sorted out, with extra categories created, you will also find parasites, protozoa, and other single celled eukaryotes in the <em>invertebrate</em> grouping.\n";
 printf "</p>\n";
 
+printf "<p>\n";
+printf "Please use the <a href='https://genome.ucsc.edu/assemblyRequest.html' target=_blank>Assembly Request</a> page to find and request GenBank assemblies that have not yet been included in the collections here.\n";
+printf "</p>\n";
+
 endHtml;