94beebccbdcae3b709516cdacd2f42e2372ebae2
jnavarr5
  Wed Sep 25 16:26:39 2019 -0700
Adding a note to other help pages about the 'useOneFile on' hub setting, refs #19383

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 7449ab1..8f1c0cc 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -195,30 +195,34 @@
   within it</li>
   <li>
   a twoBit file with your sequence if you are setting up an assembly hub.</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>
+<p>
 <strong><em>Example 1:</em></strong> Directory hierarchy for a hub containing DNase and RNAseq data 
 for the hg18 and hg19 human genome assemblies. The hg18/ and hg19/ subdirectories contain the 
 assembly-specific data files.</p>
 <pre><code>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
      dnase.html - description text for a DNase track 
      dnaseLiver.bigWig - wiggle plot of DNase in liver
      dnaseLiver.bigBed - regions of active DNase
      liverGenes.bigGenePred - gene annotations of genes over-expressed in liver tissue
      dnaseLung.bigWig - wiggle plot of DNase in lung
      dnaseLung.bigWig - regions of active DNase
@@ -338,30 +342,34 @@
 <p>
 <em>VCF</em> - VCF (Variant Call Format) files can contain annotations of single nucleotide 
 variants, insertions/deletions, copy number variants, structural variants and other types of genomic
 variation. When a VCF file is compressed and indexed using 
 <a href="http://samtools.sourceforge.net/tabix.shtml" target="_blank">tabix</a> (available 
 <a href="http://sourceforge.net/projects/samtools/files/tabix/" target="_blank">here</a>), it can be
 used as a data track file. Unlike bigWig and bigBed formats, the tabix index is in a separate file, 
 which the track hub expects to be in the same directory with the same root name as the VCF file with
 the addition of a <em>.tbi</em> suffix.  See the <a href="vcf.html">VCF Track Format</a> help page 
 for more information.</p>
 <hr>
 <p><strong>Step 2. Create the track hub directory</strong><br>
 Create a track hub directory in an Internet-accessible location on your web or ftp server. This 
 directory will contain the hub.txt and genomes.txt files that define properties of the track hub and
 a subdirectory for each of the genome assemblies covered by the hub track data.</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>
 <hr>
 <p>
 <strong>Step 3. Place the track data files in an Internet-accessible location</strong><br> 
 The data files underlying a track in a hub do not have to reside in the track hub directory or even 
 on the same server, but they must be accessible via the Internet. The track hub utility supports 
 Internet protocols such as http://, https://, and ftp://, as well as file paths relative to the hub
 directory hierarchy. The location of a track file is defined by its <em>bigDataUrl</em> tag in the 
 associated trackDb.txt file (Step 7).</p>
 <hr> 
 <p>
 <strong>Step 4. Create the hub.txt file</strong><br> 
 Within the hub directory, create a hub.txt file containing a single stanza with up to six fields 
 that define properties of the track hub:</p>
 <pre><code><strong>hub</strong> <em>hub_name</em>
 <strong>shortLabel</strong> <em>hub_short_label</em>