3c8303fc9d59eccfe9386f64fe4b4ad21275df51 brianlee Sun Jun 5 09:06:58 2022 -0700 added anchors for hub.txt settings in /hgTrackHubHelp.html #2651 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 799733f..5b35d3c 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -406,53 +406,60 @@ 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 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 +<em id="hub">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. +<em id="shortLabel">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> <p> -<em>longLabel</em> - a longer descriptive label for the track hub. Suggested maximum length is 80 +<em id="longLabel">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 +<em id="genomesFile">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> +<em id="email">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 +<em id="descriptionUrl">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 +<em id="useOneFile">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