39e3bc63e290466ec4484ccc5fb36ab94a15b232
dschmelt
  Mon Nov 9 11:35:58 2020 -0800
Readability edits and removing redundancy #26462

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 0d18b69..1b31b57 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -1,35 +1,35 @@
 <!DOCTYPE html>
 <!--#set var="TITLE" value="Track Hubs" -->
 <!--#set var="ROOT" value="../.." -->
 
 <!-- Relative paths to support mirror sites with non-standard GB docs install -->
 <!--#include virtual="$ROOT/inc/gbPageStart.html" -->
 
 <h1>Using UCSC Genome Browser Track Hubs</strong></h1>
 
 <h2>Contents</h2>
 
 <h6><a href="#Intro">What Are Track Hubs?</a></h6> 
 <h6><a href="#Assembly">What Are Assembly Hubs?</a></h6>
-<h6><a href="#View">Viewing Track Hubs in the browser</a></h6>
-<h6><a href="#Setup">Setting up your own Track Hub</a></h6>
-<h6><a href="#Debug">Debugging and updating Track Hubs</a></h6>
-<h6><a href="#Search">Setting up track item search</a></h6>
-<h6><a href="#Session">Displaying Track Hubs by URL and in sessions</a></h6>
+<h6><a href="#View">Viewing Track Hubs</a></h6>
+<h6><a href="#Sharing">Sharing Track Hubs</a></h6>
+<h6><a href="#Setup">Setting up a Track Hub</a></h6>
+<h6><a href="#Debug">Debugging Track Hubs</a></h6>
+<h6><a href="#Search">Setting up item search</a></h6>
 <h6><a href="#Register">Registering a Track Hub with UCSC</a></h6>
-<h6><a href="#Compatibility">Testing hub compatibility between genome browsers</a></h6>
+<h6><a href="#Compatibility">Checking Hub settings and Compatibility</a></h6>
 <h6><a href="#Hosting">Where to host your data</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> 
   <li>
   <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> 
   (Reference guide for trackDb parameter definitions)</li> 
   <li>
@@ -152,59 +152,65 @@
 If successful, your track hub will appear on that page.</p> 
 <p>
 Tracks accessed through a hub can be used in Genome Browser
 <a href="hgSessionHelp.html">sessions</a> and <a href="hgTracksHelp.html#CustomTracks">custom 
 tracks</a> in the same manner as other tracks. The data underlying data hub tracks can be viewed,
 manipulated, and downloaded using the <a href="../../cgi-bin/hgTables">UCSC Table Browser</a>.
 To remove a track hub from your Genome Browser display, click the &quot;Disconnect&quot; button on
 the Track Hubs page.</p>
 <p>
 For confidential or private data, please note
 that unlisted hubs are not secure. The URL helps to hide the location of the data; it is
 a simple barrier of obscurity. Please also know that hubs can be loaded from local directories
 when using <a  href="hubQuickStartAssembly.html#blatGbib">GBiB</a>.</p>
 
 <a name="Sharing"></a>
-<h3>Sharing Track Hubs</h3>
-<p>When sharing track hubs on a single assembly from manuscripts, publications,
-or on research websites, we recommend using a session to link to
-the Genome Browser view attached to that particular track hub. This has the advantage 
-of being able to save and share configuration settings made on other, native browser tracks.
-The process for generating a session link to share a track hub for a manuscript is to
-make the hub on your web-accessible server, attach the hub to the Genome Browser, configure
+<h2>Sharing Track Hubs</h2>
+<p>When sharing track hubs on a single assembly, we recommend using 
+<a href="../../cgi-bin/hgSession">Saved Sessions</a>
+(for manuscripts, publications). These have the advantage 
+of being able to save and share configuration settings made on other browser tracks.
+If you are just starting, an overview of the proces is to make the hub on 
+your web-accessible server, attach the hub to the Genome Browser, configure
 browser position and related tracks, then <a href="../../cgi-bin/hgSession">
 save your named session</a> and share the
 session link. Your session links will be in the following format with 
 your chosen username and session name:</p>
 <ul>
 <li><a href="http://genome.ucsc.edu/s/ExampleUser/TrackHubSession">
 http://genome.ucsc.edu/s/ExampleUser/TrackHubSession</a></li>
 </ul>
-<p>
-It is also possible to add or share a track hub directly by URL. If you add
-<strong>hubUrl=[URL]</strong> to your hgTracks URL line, it will add the hub directly into the 
-browser:</p>
+<p>We have additional resources about Saved Session
+<a href="hgSessionHelp.html#HowToShare" target="_blank">sharing</a> and,
+<a href="hgSessionHelp.html#Create" target="_blank">
+backup to a file</a>.</p>
+<p>
+If you prefer URL manipulation, it is also possible to add or 
+<a href="../../FAQ/FAQlink.html#hubUrl" target="_blank">share a track hub directly by URL</a> 
+or otherwise <a href="../help/customTrack.html#optParams"
+target="_blank">modify the browser via URL</a>. For example, if you add 
+<strong>hubUrl=[URL]</strong> to your hgTracks URL line, it will add the hub 
+directly into the browser:</p>
 <ul>
 <li><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt">
 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt</a></li></ul>
 <p>
 If you are adding an assembly hub with multiple genomes, you can link directly to hgGateway, 
 the assembly selection page and a particular genome:</p>
 <ul>
 <li><a href="../../cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt">
 http://genome.ucsc.edu/cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt</a></li></ul>
-
 <!-- ========== Setting Up Your Own Track Hub ============================== -->
 <a name="Setup"></a>
 <h2>Setting up your own Track Hub</h2>
 <p>
 This section provides a step-by-step description of the process used to set up a track hub on your 
 own server.</p>
 <p>
 To create your own hub you will need:</p> 
 <ul>
   <li>
   one or more data sets formatted in one of the compressed binary index formats supported by the 
   Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract,
   bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF</li>
   <li>
   a set of text files that specify properties for the track hub and for each of the data tracks 
@@ -730,81 +736,30 @@
 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
 intructions 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
 the input BED data to be case-senstive sorted (<code>sort -k1,1 -k2,2n</code>). You can use
 either the example UNIX <code>sort</code> command or the <code>bedSort</code> utility available
 <a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">here</a>. See an example
 <a href="examples/hubExamples/hubIndexedBigBedSearchable/" target="_blank">searchable hub</a>.</p>
 
-<!-- ========== Displaying Track Hubs by URL and in Sessions ============================== -->
-<a name="Session"></a>
-<h2>Displaying Track Hubs by URL and in sessions</h2>
-<p>
-Once you have successfully loaded your hub, by pasting the URL to the location of your hub.txt file 
-into the <a href="../../cgi-bin/hgHubConnect" target="_blank">My Hubs</a> tab of the Track Data Hubs
-page, you may want to consider building URLs to directly load the hub along with session 
-settings.</p>
-<p>
-To build a URL that will load the hub directly, add &quot;<b>&hubUrl=</b>&quot; to the hgTracks
-CGI followed by the address of the hub.txt file. You also need to include the UCSC assembly you
-are displaying the hub upon such as &quot;db=hg19&quot;. For example, here is a working link that
-will visualize the ENCODE AWG hub:
-<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?<b>db=hg19&hubUrl=</b>http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt </code></pre>
-<p>
-If you also want to load your hub at specific browser coordinates and with a specific set of other
-browser tracks (you can also set the visibility of each track in your hub), you can save your
-hub in a session, which are in essence &quot;View Settings&quot; collected in a text file (example
-session text files <a href="../help/examples/sessions/" target="_blank">here</a>). Sessions can be
-<a href="hgSessionHelp.html#HowToShare" target="_blank">shared</a> in different ways,
-please see the instructions for <a href="hgSessionHelp.html#Create" target="_blank">
-creating a session and saving it to a file</a>.</p>
-<p>
-By making your session file available over the Internet, you can build a URL that will load the 
-session automatically by adding &quot;<b>&hgS_loadUrlName=</b>&quot; to the hgTracks CGI followed by
-the URL location of the saved session file. The location of the saved session file should be in the 
-same directory that holds your hub.txt file. Finally add &quot;<b>&hgS_doLoadUrl=submit</b>&quot; 
-to the URL to inform the browser to load the session.</p>
-<p>
-There are four required variables for your URL to load a session with a hub and an example URL:</p>
-<pre><code><strong>db</strong> - name of the assembly (e.g. hg19 or mm10)
-<strong>hubUrl</strong> - URL to your track hub
-<strong>hgS_loadUrlName</strong> - URL to your session file
-<strong>hgS_doLoadUrl</strong> - value should be "submit" </code></pre>
-<pre>http://genome.ucsc.edu/cgi-bin/hgTracks<strong>?db=</strong>hg19<strong>&hubUrl=</strong>http://myLab.org/myHub.txt<strong>&hgS_loadUrlName=</strong>http://mySession<strong>&hgS_doLoadUrl=submit</strong> </pre>
-<p>
-Another feature one can use in place of &quot;<strong>&hubUrl=</strong>&quot; is 
-&quot;<strong>&hubClear=</strong>&quot;, which will load a hub while simultaneously disconnecting
- or clearing, hubs located at the same location. For example adding 
-<code>&hubClear=http://university.edu/lab/folder/hub10.txt</code> would connect the 
-referenced hub10.txt while simultaneously disconnecting any hubs that might be displayed from 
-the same <code>http://university.edu/lab/folder/</code> directory (for example, hub1.txt, hub2.txt, 
-ect.). This feature can be useful for dynamically generated hubs that might collect in the browser 
-otherwise.</p>
-
-<p>
-Beyond the URL options of &quot;<strong>&hubUrl=</strong>&quot; and &quot;<strong>&hubClear=</strong>&quot;
-there are many other <a href="../../FAQ/FAQlink.html" target="_blank">ways to link to the Browser</a>
-including a list of <a href="../help/customTrack.html#optParams"
-target="_blank">URL optional parameters</a> described in the the Custom Tracks User's Guide.</p>
-
 <!-- ========== Registering a Track Hub with UCSC ==================== -->
 <a name="Register"></a>
 <h2>Registering a Track Hub with UCSC</h2>
 <p>
 If you would like to share your track hub with other Genome Browser users, you can register your 
 hub with UCSC by contacting the Genome Browser technical support mailing list at 
 <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. Please include the URL of your 
 hub.txt file in the message. Once registered, your hub will appear as a link on the Public Hubs tab 
 on the Track Hubs page. To assist developers of Public Hubs, there is a 
 <a href="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines">Public Hubs Guidelines</a> 
 page. The page shares pointers and preferred style approaches, such as the need for creating 
 description html pages for your data that display any available references and an email contact for 
 further data questions.</p>
 <p>
 Alternatively, you can share your track hub with selected colleagues by providing them with the URL