32df51bb0c13175b852fe149d7514bb3c3eb0fb8
gperez2
  Wed Jul 3 10:11:15 2024 -0700
Incorporating Lou's feedback for the adding groups to a track hub documentation, refs #33580

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 0cd7e0f..7524db7 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -822,54 +822,53 @@
 <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>,
 here is how the track hub displays without the groups setting:</p>
-        <img  width="95%" height="120px" src="../../images/epdHubEx.png">
+<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
-defaultIsClosed 0 </code></pre>
+priority 1 </code></pre>
 
 <pre><code>name cage
 label CAGE
-priority 2
-defaultIsClosed 0 </code></pre>
+priority 2 </code></pre>
 
 <pre><code>name rampage
 label RAMPAGE
-priority 3
-defaultIsClosed 0  </code></pre>
+priority 3 </code></pre>
 
 <pre><code>name fantom5
 label Fantom5
 priority 4
-defaultIsClosed 0</code></pre>
+defaultIsClosed 1</code></pre>
 
 <ul>
    <li>The <b>name</b> is used in the trackDb.txt track definition group, to assign a particular track to
        a group.</li>
    <li>The <b>label</b> is displayed on the genome browser as the title of the group under the primary
        genome browser image display</li>
    <li>The <b>priority</b> orders the track group with the other track groups</li>
    <li>The <b>defaultIsClosed</b> determines if the track group is expanded or closed by default. Values to use are 0 or 1</li>
 </ul>
 
 
 <p>You would then add the group name to your tracks in the trackDb stanza. For example, adding the
 Histone Marks track to the Histone group:<p>
 <pre><code>track 1histone
 type bigWig
@@ -879,32 +878,33 @@
 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>
-        <img  width="95%" height="350px" src="../../images/epdHubGroups.png">
-
+<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
 CGI variable <em><strong>udcTimeout=5</strong></em> into the Genome Browser URL, which will reduce
 the delay to five seconds. To add this variable, open the Genome Browser tracks page and zoom or
 scroll the image to display a full browser URL in which the CGI variables visible. Insert the CGI