32df51bb0c13175b852fe149d7514bb3c3eb0fb8 gperez2 Wed Jul 3 10:11:15 2024 -0700 Incorporating Lou's feedback for the adding groups to a track hub documentation, refs #33580 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 0cd7e0f..7524db7 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -822,54 +822,53 @@ <p> Both parent and child tracks within a super-track can have their own description files. If the description file is not present, the corresponding sections of the track settings and details pages are left blank. Only one description page can be associated with composite and multiWig tracks; the file name should correspond to the symbolic name of the top-level track in the composite.</p> <!-- ========== Adding Groups to a Track hub ==================== --> <a name="Group"></a> <h2>Adding groups to a Track Hub</h2> <p>You can add groups to your track hub by using the groups setting, which points to a separate text document that defines the track groups under the primary genome browser image display. As an example using the <a href="https://epd.expasy.org/epd/ucsc/epdHub/epdHub.txt" target="_blank">EPD Viewer Hub</a>, here is how the track hub displays without the groups setting:</p> - <img width="95%" height="120px" src="../../images/epdHubEx.png"> +<div class="text-center"> + <img class='text-center' width="95%" src="../../images/epdHubEx.png"> +</div> <p>Groups such as Histone, CAGE, RAMPAGE, and Fantom5 groups can be added. The text document that defines the track groups can be named groups.txt and specifies the groups such as the following: </p> <pre><code>name histone label Histone -priority 1 -defaultIsClosed 0 </code></pre> +priority 1 </code></pre> <pre><code>name cage label CAGE -priority 2 -defaultIsClosed 0 </code></pre> +priority 2 </code></pre> <pre><code>name rampage label RAMPAGE -priority 3 -defaultIsClosed 0 </code></pre> +priority 3 </code></pre> <pre><code>name fantom5 label Fantom5 priority 4 -defaultIsClosed 0</code></pre> +defaultIsClosed 1</code></pre> <ul> <li>The <b>name</b> is used in the trackDb.txt track definition group, to assign a particular track to a group.</li> <li>The <b>label</b> is displayed on the genome browser as the title of the group under the primary genome browser image display</li> <li>The <b>priority</b> orders the track group with the other track groups</li> <li>The <b>defaultIsClosed</b> determines if the track group is expanded or closed by default. Values to use are 0 or 1</li> </ul> <p>You would then add the group name to your tracks in the trackDb stanza. For example, adding the Histone Marks track to the Histone group:<p> <pre><code>track 1histone type bigWig @@ -879,32 +878,33 @@ priority 1 compositeTrack on allButtonPair on windowingFunction mean shortLabel Histone Marks visibility full <strong>group</strong> histone</code></pre> <p>The groups.txt file then needs to be added to the genome stanza. The genome can be a UCSC genome or an assembly hub. The hg38 genome will be used as an example: <pre><code>genome hg38 trackDb hg38/trackDb.txt groups groups.txt</code></pre> <p>Attaching the EPD Viewer Hub with these group settings will then display the tracks within the groups:</p> - <img width="95%" height="350px" src="../../images/epdHubGroups.png"> - +<div class="text-center"> + <img class='text-center' width="95%" src="../../images/epdHub_Groups.png"> +</div> <!-- ========== Debugging and Updating Track Hubs ============================== --> <a name="Debug"></a> <h2>Debugging Track Hubs</strong></h2> <h3>Not updating? Change udcTimeout</h3> <p> As part of the track hub mechanism, UCSC caches data from the hub on the local server. The hub utility periodically checks the time stamps on the hub files, and downloads them again only if they have a time stamp newer than the UCSC one. For performance reasons, UCSC checks the time stamps every 300 seconds, which can result in a 5-minute delay between the time a hub file is updated and the change appears on the Genome Browser. Hub providers can work around this delay by inserting the CGI variable <em><strong>udcTimeout=5</strong></em> into the Genome Browser URL, which will reduce the delay to five seconds. To add this variable, open the Genome Browser tracks page and zoom or scroll the image to display a full browser URL in which the CGI variables visible. Insert the CGI