ae75856d0e07fd6964347b78b2e827e4f90b545e
gperez2
  Fri Jul 5 14:16:02 2024 -0700
hubClone the EPD Viewer Hub and updated the URLs to the goldenPath hubExamples, refs #34050

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 7524db7..da11064 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -820,31 +820,31 @@
 be named "dnaseSignal.html". The description file must reside in the same directory as the
 trackDb.txt file.</p> 
 <p>
 Both parent and child tracks within a super-track can have their own description files. If the 
 description file is not present, the corresponding sections of the track settings and details pages 
 are left blank. Only one description page can be associated with composite and multiWig tracks; the 
 file name should correspond to the symbolic name of the top-level track in the composite.</p>
 
 <!-- ========== Adding Groups to a Track hub ==================== -->
 <a name="Group"></a>
 <h2>Adding groups to a Track Hub</h2>
 
 <p>You can add groups to your track hub by using the groups setting, which points to a separate
 text document that defines the track groups under the primary genome browser image display. As an
 example using the
-<a href="https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt" target="_blank">EPD Viewer Hub</a>,
+<a href="examples/hubExamples/epdHub/epdHub.txt" target="_blank">EPD Viewer Hub</a>,
 here is how the track hub displays without the groups setting:</p>
 <div class="text-center">
         <img class='text-center' width="95%" src="../../images/epdHubEx.png">
 </div>
 
 <p>Groups such as Histone, CAGE, RAMPAGE, and Fantom5 groups can be added. The text document that
 defines the track groups can be named  groups.txt and specifies the groups such as the following:
 </p>
 <pre><code>name histone
 label Histone
 priority 1 </code></pre>
 
 <pre><code>name cage
 label CAGE
 priority 2 </code></pre>
@@ -876,32 +876,33 @@
 autoScale on
 smoothingWindow 10
 priority 1
 compositeTrack on
 allButtonPair on
 windowingFunction mean
 shortLabel Histone Marks
 visibility full
 <strong>group</strong> histone</code></pre>
 
 <p>The groups.txt file then needs to be added to the genome stanza. The genome can be a UCSC genome or an assembly hub. The hg38 genome will be used as an example:
 <pre><code>genome hg38
 trackDb hg38/trackDb.txt
 groups groups.txt</code></pre>
 
-<p>Attaching the EPD Viewer Hub with these group settings will then display the tracks within
-the groups:</p>
+<p>Attaching the
+<a href="examples/hubExamples/hubGroupings/epdHub/epdHub.txt" target="_blank">EPD Viewer Hub</a>,
+with these group settings will then display the tracks within the groups:</p>
 <div class="text-center">
         <img class='text-center' width="95%" src="../../images/epdHub_Groups.png">
 </div>
 
 <!-- ========== Debugging and Updating Track Hubs ============================== -->
 <a name="Debug"></a>
 <h2>Debugging Track Hubs</strong></h2>
 
 <h3>Not updating? Change udcTimeout</h3>
 <p>
 As part of the track hub mechanism, UCSC caches data from the hub on the local server. The hub
 utility periodically checks the time stamps on the hub files, and downloads them again only if they
 have a time stamp newer than the UCSC one. For performance reasons, UCSC checks the time stamps
 every 300 seconds, which can result in a 5-minute delay between the time a hub file is updated and
 the change appears on the Genome Browser. Hub providers can work around this delay by inserting the