f50fbe16a5fe95c1e0c1a84e88b689f06e9c682f
gperez2
  Fri Sep 26 17:46:49 2025 -0700
Replacing the Assembly Hub wiki links with the new Assembly Hub User Guide page, refs #34740

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index d22d7f638c4..3300cd5bfd1 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -19,32 +19,31 @@
 <h6><a href="#Search">Setting up item search</a></h6>
 <h6><a href="#Filters">Adding filters to your Track Hub</a></h6>
 <h6><a href="#Register">Registering a Track Hub with UCSC</a></h6>
 <h6><a href="#Compatibility">Checking Hub settings and compatibility</a></h6>
 <h6><a href="#Hosting">Where to host your data</a></h6>
 <h6><a href="https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html"
       target = _blank>Track Hub Database Definition Document</a></h6>
 <hr>
 <p>
 <strong>Additional resources</strong></p> 
 <ul>
   <li>Raney BJ, et al. <a href="https://doi.org/10.1093/bioinformatics/btt637"
   target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on 
   the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. 
   <li> 
-  <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hubs 
-  Wiki</a></li> 
+  <a href="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</a></li>
   <li>
   <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> 
   (Reference guide for trackDb parameter definitions)</li> 
   <li><a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/" target=
   "_blank">Track hub settings blog post</a></li>
   <li>
   <a href="publicHubGuidelines.html" target="_blank">Public Hub Guidelines</a></li>
   <li>
   <a href="hubQuickStart.html" target="_blank">Quick Start Guide to Basic Hubs</a></li> 
   <li>
   <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into
   Groupings</a></li> 
   <li>
   <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs with 
   Blat</a></li> 
@@ -113,32 +112,32 @@
 the persistence of their data, or would like to take full advantage of track functionality, or 
 create a browser on sequence not natively supported by UCSC or a genome browser mirror, track hubs 
 are a better solution. Both mechanisms give data providers the flexibility to directly add, update, 
 and remove data from their display as needed.</p>
 
 <!-- ========== What Are Assembly Hubs? ============================== -->
 <a name="Assembly"></a>
 <h2>What Are Assembly Hubs?</h2> 
 <p> 
 Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted 
 natively on the Browser. Assembly Data Hubs were developed to address the increasing need for 
 researchers to annotate sequence for which UCSC does not provide an annotation database. They allow 
 researchers to include the underlying reference sequence, as well as data tracks that annotate that 
 sequence. Sequence is stored in the UCSC twoBit format, and the annotation tracks are stored in the 
 same manner as Track Data Hubs. For more information on how to setup your own Assembly Data Hub, 
-please refer to the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hub 
-wiki</a> and see the <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to 
+please refer to the <a href="assemblyHubHelp.html">Assembly Hub User Guide</a> and see the
+<a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to
 Assembly Hubs</a>.</p>
 
 <!-- ========== Viewing Hub Tracks in the Browser ==================== -->
 <a name="View"></a>
 <h2>Viewing Track Hubs</h2> 
 <h3>Public hubs</h3>
 <p>
 The Genome Browser provides links to a collection of public track hubs that have been registered 
 with UCSC. To view a list of the public track hubs available, click into the blue navigation bar 
 &quot;My Data&quot; and then &quot;Track Hubs&quot; to reach the 
 <a href="../../cgi-bin/hgHubConnect?#publicHubs">Public Track Hubs page</a>.
 You can click links in the &quot;Description&quot; column to see details about a particular Hub.
 To view a hub's data, click on an assembly name on the row of your 
 hub or the &quot;Connect&quot; button. If you clicked the &quot;Connect&quot; button, 
 choose your assembly or click the &quot;Genome Browser&quot; link from the top blue bar to be brought to the