6d1c72eb5d13c0c9bd80170aa0131fd47d1edf90 hiram Fri Nov 18 15:39:46 2022 -0800 add discussion about how to make your track hub appear on a GenArk assembly hub refs #30297 diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html index 2a0039c..5df7a0a 100755 --- src/hg/htdocs/goldenPath/help/hgTracksHelp.html +++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html @@ -20,30 +20,31 @@ <h6><a href="#IndivTracks">Annotation track descriptions</a></h6> <h6><a href="#BLATAlign">Using BLAT alignments</a></h6> <h6>Getting Started with:</h6> <ul> <li> <h6><a href="#GetStarted">Genome Browser Gateway</a></h6> <li> <h6><a href="#TableBrowser">Table Browser</a></h6> <li> <h6><a href="#Sessions">Using Sessions</a></h6> <li> <h6><a href="hgGeneGraph.html">Gene and Pathway Viewer</a></h6> <li> <h6><a href="#GenomeGraphs">Genome Graphs</a></h6> </ul> <h6><a href="#TrackFormatDNA">DNA text formatting</a></h6> <h6><a href="#Convert">Converting data between assemblies</a></h6> <h6><a href="#Download">Downloading genome data</a></h6> <h6><a href="#CustomTracks">Creating and managing custom annotation tracks</a></h6> <h6><a href="#TrackHubs">Getting started on Track Hubs</a></h6> +<h6><a href="#GenArkTrackHubs">Track Hubs for <em>GenArk</em> assembly hub</a></h6> <h6><a href="#UseOneFile">Track Hubs in a single file</a></h6> <h6><a href="#VisiGeneHelp">Using the VisiGene Image Browser</a></h6> </div> <div class="col-md-8"> <form name="googleForm1" method="get" action="https://www.google.com/search" onSubmit="document.googleForm1.q.value=document.googleForm1.qq.value+' site:genome.ucsc.edu/goldenPath/help';"> <p> Search the Genome Browser help pages: <input type="hidden" name="q" value=""> <input type="hidden" name="num" value="10"> <input type="hidden" name="filter" value="0"> <input type=text name=qq size=30 maxlength=255 value=""> <input type="submit" value="Submit"> </p> @@ -1446,30 +1447,62 @@ Browser interface. Browser users can display tracks from any public track hub that has been registered with UCSC. We offer <a href="publicHubGuidelines.html" target="_blank"> guidelines</a> for those who want to make a hub a public track hub. Additionally, users can import data from unlisted hubs or can set up, display, and share their own track hubs.</p> <p> For information on using the Track Hub features, refer to the <a href="hgTrackHubHelp.html">Genome Browser Track Hub User Guide</a>. For specific information on configuring your trackDb.txt file, refer to the <a href="trackDb/trackDbHub.html">Track Database Definition Document</a>. See also the <a href="hubQuickStart.html" target="_blank">Basic Hub Quick Start Guide</a>, <a href="hubQuickStartGroups.html" target="_blank">Quick Start Guide to Organizing Track Hubs into Groupings</a>, <a href="https://genome-blog.soe.ucsc.edu/blog/2022/06/28/track-hub-settings/" target="_blank">Track hub settings blog post</a>, <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a> and <a href="hubQuickStartSearch.html" target="_blank">Quick Start Guide to Searchable Track Hubs</a>.</p> +<a name="GenArkTrackHubs"></a> +<h2>Track Hubs for <em>GenArk</em> assembly hub</h2> +<p> +To construct a track hub that will display on a +<a href='https://hgdownload.soe.ucsc.edu/hubs/' +target=_blank>GenArk Assembly</a> hub, specify the <em>GenArk</em> assembly +name in the <b>genome</b> statement in your <b>hub.txt</b> file as +<a href='#UseOneFile'>described below</a>. +For example, a reference such as: +</p> +<pre> +genome GCA_021951015.1 +</pre> +<p> +will direct your track hub to display on the human +<b>Feb. 2022 - GCA_021951015.1 - HG002.mat.cur.20211005</b> genome assembly. +</p> +<p> +To share your track hub with your audience of interest, when you publish +the URL to your track hub, that <b>genome</b> reference in your track hub.txt +file will cause that associated assembly hub to display in the genome +browser with your track hub annotations on that genome browser. There is no +need to otherwise reference the assembly hub, it will automatically attach +itself. +</p> +<p> +A complete list of all available <em>GenArk</em> assemblies available can +be seen in the text file +<a href='https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt' +target=_blank>UCSC_GI.assemblyHubList.txt</a>. +</p> + <a name="UseOneFile"></a> <h2>Track Hubs in a single file</h2> <p> Historically, a hub needed a set of text files to specify properties for a track hub and each of the data tracks within the hub. The track hub settings were stored in a three file structure: hub.txt, genomes.txt, and trackDb.txt</p> <pre> 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 </pre> <p> Now, there is a trackDb option to have your entire track hub inside of one file,