3c1e958a16b6d79f859d0f51368d767acce0457c gperez2 Wed Jan 7 19:49:26 2026 -0800 Added some text and chromAlias/chromAuthority link to help pages, refs #33014 diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html index 78b7466b30e..58dd48fb4b3 100755 --- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html +++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html @@ -51,30 +51,36 @@ <strong>STEP 3:</strong> Congratulations! Your assembly hub should display!</p> <p> If you are having problems, be sure all your files and the directories are publicly accessible. You may also wish to <a href="../../cgi-bin/cartReset" target="_blank">reset</a> the browser occasionally to clear all existing data. For hubs to work, your server must also accept byte-ranges. You can check using the following command to verify "Accept-Ranges: bytes" displays: <pre><code>curl -I http://yourURL/hub.txt</code></pre></p> <p> Now that you have the assembly hub copied from above, you can copy the directory and start to edit some of the documents such as genomes.txt, groups.txt, and trackDb.txt to understand how they work. Refer to the <a href="assemblyHubHelp.html" target="_blank">Assembly Hub User Guide</a> to understand how to build a <a href="twoBit.html" target="_blank">twoBit</a> file for your own original fasta files. Read more about <a href="trackDb/trackDbHub.html" target="_blank">trackDb settings</a> in the definition document.</p> <p> +Assembly hubs also support <a href="assemblyHubHelp.html#chromAlias" +target="_blank">chromAlias and chromAuthority</a>, which let the Browser map chromosome names +across different naming schemes and display a preferred convention. A default naming scheme can be +set using the <code>chromAuthority</code> setting. +</p> +<p> This assembly hub is a an abbreviated version of a larger plant assembly Public Hub. You can explore the larger hub structure <a href="http://genome-test.soe.ucsc.edu/~hiram/hubs/Plants/" target="_blank">here</a>.</p> <p> Please note that the Browser waits 5 minutes before checking for any changes to these files. <strong>When editing hub.txt, genomes.txt, trackDb.txt, and related hub files, shorten this delay by adding <code>udcTimeout=1</code> to your URL.</strong> For more information, please see the <a href="hgTrackHubHelp.html#Debug" target="_blank">Debugging and Updating Track Hubs</a> section of the <a href="hgTrackHubHelp.html" target="_blank">Track Hub User Guide</a>. Also, for more detailed instructions on setting up a regular hub, please see the <a href="hgTrackHubHelp.html#Setup" target="_blank">Setting Up Your Own Track Hub</a> section of the Track Hub User Guide.</p> <h2>Setting up Blat and In-Silico PCR for an Assembly Hub</h2> <p> By running gfServers from your institution, you can enable blat on your assembly hubs. See