09cce8bb976575739c209813484c77126ca6a427
mspeir
  Mon Jan 6 13:23:47 2025 -0800
adding note about hubClone to page, refs #25572

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 00cceb5..bda9cc9 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -989,45 +989,73 @@
 Here is the usage statement for the hubCheck utility:
 <pre><code>hubCheck - Check a track data hub for integrity.
 usage:
    hubCheck http://yourHost/yourDir/hub.txt
 options:
    -checkSettings        - check trackDb settings to spec
    -version=[v?|url]     - version to validate settings against
                                      (defaults to version in hub.txt, or current standard)
    -extra=[file|url]     - accept settings in this file (or url)
    -level=base|required  - reject settings below this support level
    -settings             - just list settings with support level
                            Will create this directory if not existing
    -noTracks             - don't check remote files for tracks, just trackDb (faster)
    -udcDir=/dir/to/cache - place to put cache for remote bigBeds and bigWigs </code></pre></p>
 <p>
-Note that you will have to use the udcDir if /tmp/udcCache is not writable on your machine.</p>
+Note that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.</p>
 <p>
 The hubCheck program is available from the UCSC downloads server at 
 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a>.</p>
 
 <a name="troubleConnecting"></a>
 <h3>Troubleshooting Track Hub connections</h3>
 <p>
 If the browser is unable to load a track hub, it will display an error message. Some common causes
 for an import to fail include typos in the URL, a hub server that is offline, 
 or errors in the track hub configuration files. Occasionally, remote track
 hubs may be missing, off-line, or otherwise unavailable. If a user is
 already browsing data from the remote hub when it disconnects, a yellow error message will be
 displayed instead of the expected data.</p>
 
+<a name="hubClone"></a>
+<h3>Download all files in a hub using hubClone utility</h3>
+<p>
+You can use the command-line utility <em>hubClone</em> to download all of the
+data and configuration files for a hub onto your local machine. To do so, use
+the utility with the &quot;-download&quot; option and it will download any
+files specified by bigDataUrls (e.g. bigBed, bigWig, etc). By default, it only copies the
+configuration files and changes any local bigDataUrls into remote URLs. Beyond
+that, you may also find it useful to make a copy of a public hub's configuration
+files in order to imitate various settings, such as filters, search options,
+or track groupings.
+
+<p>
+Here is the usage message for the hubClone utility:
+<pre><code>hubClone - Clone the remote hub text files to a local copy in newDirectoryName, fixing up bigDataUrls to remote location if necessary
+usage:
+   hubClone http://url/to/hub.txt
+options:
+   -udcDir=/dir/to/udcCache   Path to udc directory
+   -download                  Download data files in addition to the hub configuration files
+</code></pre></p>
+
+<p>
+Note that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.</p>
+<p>
+The hubClone program is available from the UCSC downloads server at
+<a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a>.</p>
+
 <!-- ========== Setting Up Track Item Search ============================== -->
 <a name="Search"></a>
 <h2>Setting up track item search</h2>
 <p> 
 The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support 
 this behavior you have to add an index to the bigBed file when you initially create the the bigBed 
 file from the bed file input. Indices are usually created on the name field of the bed, but can be 
 created on any field of the bed. Free-text searches can also be enabled by creating a 
 <a href="trix.html">TRIX index file</a> that maps id's in the track to free-text metadata. Further
 instructions can be found in the <a href="hubQuickStartSearch.html">Searchable Hub Quick Start 
 Guide</a>.</p>
 <p>
 See the searchIndex and searchTrix fields in the <a href="trackDb/trackDbHub.html">Hub Track 
 Database Definition document</a> for 
 information on how to set up your bigBed to enable searching. The searchIndex setting requires