982d69ac4a666c4ff32f7ed167f788b81d960285
hiram
  Wed Jun 17 12:30:05 2020 -0700
reduce the vertical space consumed by options and explanations refs #25555

diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index e2ee199..719c1a2 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -114,90 +114,93 @@
 <h1>$Name Genomes assembly hubs</h1>
 <p>
 Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage.
 </p>
 
 END
 }
 
 print <<"END"
 <h3>How to view the hub</h3>
 <p>
 Options:
 <ol>
   <li>The links to the genome browser in the table below will attach that
       one specific assembly to the genome browser.  This is most likely what
-      you want.</li>
-  <li>Instead, you can attach the entire set of assemblies as one group to
-      the genome browser with the following links depending upon which of
-      our mirror site browsers you prefer to use:
-    <ul>
-    <li><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
-        target="_blank">genome.ucsc.edu</a></li>
-    <li><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
-        target="_blank">genome-euro.ucsc.edu</a></li>
-    <li><a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
-        target="_blank">genome-asia.ucsc.edu</a></li>
-    </ul>
+      you want.  Alternatively, the entire set of assemblies can be attached
+      as one group to the genome browser with the following links depending
+      upon which of our mirror site browsers you prefer to use:
+<table border="1">
+<tr>
+  <th>attach all assemblies to selected site:</th>
+  <th>&nbsp;</th>
+  <th><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
+        target="_blank">genome.ucsc.edu</a></th>
+  <th>&nbsp;</th>
+  <th><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
+        target="_blank">genome-euro.ucsc.edu</a></th>
+  <th>&nbsp;</th>
+  <th><a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&amp;genome=$defaultAssembly"
+        target="_blank">genome-asia.ucsc.edu</a></th>
+</tr>
+</table>
   </li>
   <li>To manually attach all the assemblies in this hub to genome browsers
       that are not one of the three UCSC mirror sites:
     <ol>
       <li>From the blue navigation bar, go to
     <em><strong>My Data</strong> -&gt; <strong>Track Hubs</strong></em></li>
       <li>Then select the <strong>My Hubs</strong> tab and enter this URL into
           the textbox:
     <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt</code></li>
       <li> Once you have added the URL to the entry form,
            press the <em><strong>Add Hub</strong></em> button to add the hub.</li>
     </ol>
   </li>
 </ol>
 </p>
 
 <p>
 After adding the hub, you will be redirected to the gateway page.  The
 genome assemblies can be selected from the
 <em>${Name} Hub Assembly</em> dropdown menu.
 Instead of adding all the assemblies in one collected group, use the individual
 <em>view in browser</em> in the table below.
 </p>
 <h3>See also: <a href='asmStats.html'>assembly statistics</a>,&nbsp;<a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br>
 <h3>Data resource links</h3>
-<p>
 NOTE: <em>Click on the column headers to sort the table by that column</em><br>
-The <em>common name/view in browser</em> will attach only that single assembly to
+The <em>common name and view in browser</em> will attach only that single assembly to
 the genome browser.<br>
-The <em>scientific name/and data download</em> link provides access to the files for that one
+The <em>scientific name and data download</em> link provides access to the files for that one
 assembly hub.<br>
-The <em>class/VGP link</em> provides access to the VGP GenomeArk page for that genome<br>
+The <em>class VGP link</em> provides access to the VGP GenomeArk page for that genome.<br>
 The other links provide access to NCBI resources for these assemblies.
-</p>
 END
 }	#	sub startHtml()
 
 ##############################################################################
 ### start the table output
 ##############################################################################
 sub startTable() {
 print '
 <table class="sortable" border="1">
 <thead><tr><th>count</th>
   <th>common&nbsp;name&nbsp;and<br>view&nbsp;in&nbsp;browser</th>
   <th>scientific name<br>and&nbsp;data&nbsp;download</th>
   <th>NCBI&nbsp;assembly</th>
-  <th>bioSample</th><th>bioProject</th>
+  <th>BioSample</th><th>BioProject</th>
   <th>assembly&nbsp;date,<br>source&nbsp;link</th>
 ';
 
 if ($vgpIndex) {
   printf "<th>class<br>VGP&nbsp;link</th>\n";
 }
 print "</tr></thead><tbody>\n";
 }	#	sub startTable()
 
 ##############################################################################
 ### end the table output
 ##############################################################################
 sub endTable() {
 
 print <<"END"
@@ -289,30 +292,32 @@
         }
       }
     }
     close (FH);
     my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId";
     printf "<tr><td align=right>%d</td>\n", ++$rowCount;
 ###    printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/hub.txt&amp;genome=%s&amp;position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $accessionId, $commonName;
     printf "<td align=center><a href='https://genome.ucsc.edu/h/%s' target=_blank>%s</a></td>\n", $accessionId, $commonName;
     printf "    <td align=center><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName;
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s</a></td>\n", $gcPrefix, $asmAcc, $asmId;
     if ( $bioSample ne "notFound" ) {
     printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample;
     } else {
     printf "    <td align=left>n/a</td>\n";
     }
+    # one broken assembly_report
+    $bioProject= "PRJEB25768" if ($accessionId eq "GCA_900324465.2");
     if ($bioProject eq "notFound") {
       printf "    <td align=left>%s</td>\n", $bioProject;
     } else {
       printf "    <td align=left><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>\n", $bioProject, $bioProject;
     }
     printf "    <td align=center><a href='%s' target=_blank>%s</a></td>\n", $ncbiFtpLink, $asmDate;
     if ($vgpIndex) {
       my $sciNameUnderscore = $sciName;
       $sciNameUnderscore =~ s/ /_/g;
       $sciNameUnderscore = "Strigops_habroptilus" if ($sciName =~ m/Strigops habroptila/);
 
       if (! defined($vgpClass{$asmId})) {
          printf STDERR "# ERROR: no 'class' defined for VGP assembly %s\n", $asmId;
          exit 255;
       }