b4aec3faf165901efc9fd333ba77f71c40da4e55 brianlee Fri Jun 3 06:45:47 2022 -0700 adding useOneFile on doc to trackDbHub page #26512 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 281d3e8..799733f 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -396,31 +396,31 @@ 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> +<strong id="hub.txt">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> <strong>longLabel</strong> <em>hub_long_label</em> <strong>genomesFile</strong> <em>genomes_filelist</em> <strong>email</strong> <em>email_address</em> <strong>descriptionUrl</strong> <em>descriptionUrl</em> </code></pre> <p> <em>hub</em> - a single-word name of the directory containing the track hub files. Not displayed to hub users. This must be the first line in the hub.txt file.</p> <p> <em>shortLabel</em> - the short name for the track hub. Suggested maximum length is 17 characters. Displayed as the hub name on the Track Hubs page and the track group name on the browser tracks page.</p> @@ -428,30 +428,39 @@ <em>longLabel</em> - a longer descriptive label for the track hub. Suggested maximum length is 80 characters. Displayed in the description field on the Track Hubs page.</p> <p> <em>genomesFile</em> - the relative path of the genomes.txt file, which contains the list of genome assemblies covered by the track data and the names of their associated configuration files. By convention the genomes.txt file is located in the same directory as the hub.txt file.</p> <p> <em>email</em> - the contact to whom questions regarding the track hub should be directed.</p> <p> <em>descriptionUrl</em> - URL to HTML page with a description of the hub's contents. This can be relative to the directory which holds hub.txt. This file is assumed to be HTML, and if the hub is a UCSC public hub, this HTML will be crawled nightly by UCSC to build an index with which public hubs can be searched. If present, clicks on the shortLabel will open this HTML in a new tab. This field is optional.</p> <p> +<em>useOneFile on</em> - only use this setting if your hub is only displaying one genome and +if you wish to put all information into only one file: hub.txt. This setting allows you +to put the text lines of <a target="_blank" href="#genomes.txt"><code>genomes.txt</code></a> +and<a target="_blank" href="#trackDb.txt"><code>trackDb.txt</code></a> all into the singular +<a target="_blank" href="#hub.txt"><code>hub.txt</code></a>file. To learn more about +this setting click <b><a target="_blank" href="hgTracksHelp.html#UseOneFile"><code>useOneFile on</code></a></b> +and see a <a href="examples/hubExamples/hubUseOneFile/singleFileHubExample.txt" +target="_blank">working example here</a>.</p> +<p> <strong><em>Example 2:</em></strong> Sample hub.txt file defining attributes for the track hub shown in <em>Example 1</em>.</p> <pre><code><strong>hub</strong> UCSCHub <strong>shortLabel</strong> UCSC Hub <strong>longLabel</strong> UCSC Genome Informatics Hub for human DNase and RNAseq data <strong>genomesFile</strong> genomes.txt <strong>email</strong> genome@soe.ucsc.edu <strong>descriptionUrl</strong> ucscHub.html </code></pre> <hr> <a name="genomes.txt"></a> <p> <strong>Step 5. Create the genomes.txt file</strong><br> Create a genomes.txt file within the track hub directory that contains a two-line stanza that must be separated by a line for each genome assembly that is supported by the hub data. Each stanza shows the location of the trackDb file that defines display properties for each track in that