7840f74333c846da8abef1701b16feb74e8f334c
dschmelt
  Wed Nov 20 11:09:00 2019 -0800
Adding links and allowed char set #24490

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 6335988..19ac6f1 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -187,31 +187,32 @@
 <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 
   within it</li>
   <li>
-  a twoBit file with your sequence if you are setting up an assembly hub.</li>
+  a twoBit file with your sequence if you are setting up an assembly hub. Note that the allowed
+  characters in sequence names are [A-Za-z_0-9_.-]</li>
   <li>
   an Internet-enabled web server or ftp server </li>
   <!--Question: do we have some general minimum requirements for this?-->
 </ul>
 <p>
 The files are placed on the server in a file hierarchy like the one shown in <em>Example 1</em>. 
 Users experienced in setting up Genome Browser mirrors that contain their own data will find that 
 setting up a track hub is similar, but is usually much easier. Depending on the number and 
 complexity of the data sets, a track hub can typically be set up in a day or two. It is generally 
 easiest to run the command-line data formatting programs in a Linux programming environment, 
 although it's possible to manipulate smaller data sets using Mac OS-X as well.</p>
 <p>
 <b>Note:</b> there is now a <code>useOneFile on</code> hub setting that allows the hub
 properties to be specified in a single file. More information about this setting can be found on the
 <a href="./hgTracksHelp.html#UseOneFile" target="_blank">Genome Browser User Guide</a>.</p>
@@ -666,33 +667,36 @@
    -udcDir=/dir/to/cache - place to put cache for remote bigBeds and bigWigs </code></pre>
 <p>
 Note that you will have to use the udcDir 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>
 
 <!-- ========== 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.</p>
+<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 Hub Track Database Definition document for 
+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>