6d1c72eb5d13c0c9bd80170aa0131fd47d1edf90
hiram
  Fri Nov 18 15:39:46 2022 -0800
add discussion about how to make your track hub appear on a GenArk assembly hub refs #30297

diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html
index 2a0039c..5df7a0a 100755
--- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html
@@ -20,30 +20,31 @@
 <h6><a href="#IndivTracks">Annotation track descriptions</a></h6>
 <h6><a href="#BLATAlign">Using BLAT alignments</a></h6>
 <h6>Getting Started with:</h6>
 <ul>
   <li> <h6><a href="#GetStarted">Genome Browser Gateway</a></h6>
   <li> <h6><a href="#TableBrowser">Table Browser</a></h6>
   <li> <h6><a href="#Sessions">Using Sessions</a></h6>
   <li> <h6><a href="hgGeneGraph.html">Gene and Pathway Viewer</a></h6>
   <li> <h6><a href="#GenomeGraphs">Genome Graphs</a></h6>
 </ul>
 <h6><a href="#TrackFormatDNA">DNA text formatting</a></h6>
 <h6><a href="#Convert">Converting data between assemblies</a></h6>
 <h6><a href="#Download">Downloading genome data</a></h6>
 <h6><a href="#CustomTracks">Creating and managing custom annotation tracks</a></h6>
 <h6><a href="#TrackHubs">Getting started on Track Hubs</a></h6>
+<h6><a href="#GenArkTrackHubs">Track Hubs for <em>GenArk</em> assembly hub</a></h6>
 <h6><a href="#UseOneFile">Track Hubs in a single file</a></h6>
 <h6><a href="#VisiGeneHelp">Using the VisiGene Image Browser</a></h6>
 
 </div>
 <div class="col-md-8">
 
 <form name="googleForm1" method="get" action="https://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+'   site:genome.ucsc.edu/goldenPath/help';">
   <p>
   Search the Genome Browser help pages: &nbsp;
   <input type="hidden" name="q" value="">
   <input type="hidden" name="num" value="10">
   <input type="hidden" name="filter" value="0">
   <input type=text name=qq size=30 maxlength=255 value="">
   <input type="submit" value="Submit">
   </p>
@@ -1446,30 +1447,62 @@
 Browser interface. Browser users can display tracks from any public track hub that has been
 registered with UCSC. We offer <a href="publicHubGuidelines.html" target="_blank"> guidelines</a>
 for those who want to make a hub a public track hub. Additionally, users can import data from
 unlisted hubs or can set up, display, and share their own track hubs.</p>
 <p>
 For information on using the Track Hub features, refer to the <a href="hgTrackHubHelp.html">Genome
 Browser Track Hub User Guide</a>. For specific information on configuring your trackDb.txt file,
 refer to the <a href="trackDb/trackDbHub.html">Track Database Definition Document</a>. See also the
 <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a>,
 <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into
 Groupings</a>, <a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/"
 target="_blank">Track hub settings blog post</a>, <a href="hubQuickStartAssembly.html"
 target="_blank">Quick Start Guide to Assembly Hubs</a> and <a href="hubQuickStartSearch.html"
 target="_blank">Quick Start Guide to Searchable Track Hubs</a>.</p>
 
+<a name="GenArkTrackHubs"></a>
+<h2>Track Hubs for <em>GenArk</em> assembly hub</h2>
+<p>
+To construct a track hub that will display on a
+<a href='https://hgdownload.soe.ucsc.edu/hubs/'
+target=_blank>GenArk Assembly</a> hub, specify the <em>GenArk</em> assembly
+name in the <b>genome</b> statement in your <b>hub.txt</b> file as
+<a href='#UseOneFile'>described below</a>.
+For example, a reference such as:
+</p>
+<pre>
+genome GCA_021951015.1
+</pre>
+<p>
+will direct your track hub to display on the human
+<b>Feb. 2022 - GCA_021951015.1 - HG002.mat.cur.20211005</b> genome assembly.
+</p>
+<p>
+To share your track hub with your audience of interest, when you publish
+the URL to your track hub, that <b>genome</b> reference in your track hub.txt
+file will cause that associated assembly hub to display in the genome
+browser with your track hub annotations on that genome browser.  There is no
+need to otherwise reference the assembly hub, it will automatically attach
+itself.
+</p>
+<p>
+A complete list of all available <em>GenArk</em> assemblies available can
+be seen in the text file
+<a href='https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt'
+target=_blank>UCSC_GI.assemblyHubList.txt</a>.
+</p>
+
 <a name="UseOneFile"></a>
 <h2>Track Hubs in a single file</h2>
 <p>
 Historically, a hub needed a set of text files to specify properties for a track hub and each of
 the data tracks within the hub. The track hub settings were stored in a three file structure:
 hub.txt, genomes.txt, and trackDb.txt</p>
 <pre>
 myHub/          - directory containing track hub files
 * hub.txt       - a short description of hub properties
 * genomes.txt   - list of genome assemblies included in the hub data
 * hg19/         - directory of data for the hg19 (GRCh37) human assembly
 ** trackDb.txt  - display properties for tracks in this directory
 </pre>
 <p>
 Now, there is a trackDb option to have your entire track hub inside of one file,