631a7882f8c689b66f3d81fc8f25fbf98f73499a
hiram
  Mon Oct 2 16:55:41 2023 -0700
remove the all genomes at once attachment option refs #29545

diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
index 4414bf6..e72a403 100755
--- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
+++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
@@ -156,76 +156,38 @@
 <!--#set var="TITLE" value="$Name genomes assembly hubs" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" -->
 
 <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>
+<h3>How to view the assembly of interest</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.  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>
+The links to the genome browser in the table below will attach that
+one specific assembly to the genome browser.  Use the links in
+the column labeled <b>common name and view in browser</b> to view that
+assembly in the genome browser.
 </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>
 END
 
 if ($vgpIndex) {
   print <<"END";
 <h3>Listings:</h3>&nbsp;&nbsp;<b>(from RepeatModeler masking)</b>
 <p>
 <ul>
 <li><a href='modeler.families.urls.txt' target=_blank>families fasta.gz</a> list of URLs for the custom library created by the RepeatModeler run</li>
 <li><a href='modeler.2bit.urls.txt' target=_blank>assembly 2bit file list</a> of URLs as masked with the RepeatModeler + <b>TRF/simpleRepeats</b> with period of 12 or less</li>
 <li><a href='rmod.log.file.list.txt' target=_blank>the rmod.log files from each RepeatModeler run</a></li>
 <li><a href='default.twoBit.file.list.txt' target=_blank>default GenArk 2bit file list</a> of URLs as masked with the ordinary RepeatMasker + <b>TRF/simpleRepeats</b> with period of 12 or less</li>
 <li><a href='modeler.table.txt' target=_blank>this data table in tab-separated</a> file text format (including TBD not working yet, or in VGP collection but not on the alignment list)</li>
 </ul>
 </p>