9f28c7f69e700fa77ab91e4f4c3f3fe2432e4b8f
lrnassar
  Wed Jun 25 12:58:23 2025 -0700
Beginning to phase our GBiB mentions for docker, refs #35611

diff --git src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
index 7c5476c5f67..18521bfd542 100755
--- src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
+++ src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
@@ -48,31 +48,36 @@
     <li><a href="#configuringDynamicGfServer">Configuring Assembly Hubs to Use a Dynamic gfServer</a>
         <ul style="margin-left: 20px;">
             <li><a href="#checkGfServerStatusForDynamicServers">Check gfServer Status for Dynamic Servers</a></li>
         </ul>
     </li>
 </ul>
 
 <a id="overview"></a>
 <h2>Overview</h2>
 <p>
     The Assembly Hub function allows you to display your novel genome sequence using the UCSC Genome Browser.
 </p>
 
 <a id="webServer"></a>
 <h2>Web Server</h2>
-<p>To display your novel genome sequence, use a web server at your institution (or free services like <a href="https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting">Cyverse</a>), for usage behind a firewall you can also load them locally through <a href="https://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html#blatGbib">GBiB</a> to supply your files to the UCSC Genome Browser. Note that hosting hub files on HTTP is highly recommended and much more efficient than FTP. You then establish a hierarchy of directories and files to host your novel genome sequence. For example:</p>
+<p>To display your novel genome sequence, use a web server at your institution (or free services 
+like <a href="https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting">Cyverse</a>), 
+for usage behind a firewall you can also load them locally through <a href="docker.html">docker</a> 
+to supply your files to the UCSC Genome Browser. Note that hosting hub files on HTTP is highly 
+recommended and much more efficient than FTP. You then establish a hierarchy of directories and 
+files to host your novel genome sequence. For example:</p>
 
 <pre style="margin-left: 20px;">
 myHub/ - directory to organize your files on this hub
     hub.txt - primary reference text file to define the hub, refers to:
     genomes.txt - definitions for each genome assembly on this hub
         newOrg1/ - directory of files for this specific genome assembly
             newOrg1.2bit - ‘2bit’ file constructed from your fasta sequence
             description.html - information about this assembly for users
             trackDb.txt - definitions for tracks on this genome assembly
             groups.txt - definitions for track groups on this assembly
             bigWig and bigBed files - data for tracks on this assembly
             external track hub data tracks
 </pre>
 <p>The URL to reference this hub would be: http://yourLab.yourInstitution.edu/myHub/hub.txt</p>
 <p><b>Note:</b> there is now a <code>useOneFile</code> on 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="https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#UseOneFile">Genome Browser User Guide</a>.</p>
@@ -279,31 +284,32 @@
 <p>Please see <a href="http://example.com/running-gfserver">Running your own gfServer</a> for details on installing and configuring both dedicated and dynamic gfServers.</p>
 <ul>
     <li>Next edit your genomes.txt stanza that references yourAssembly to have two lines to inform the browser of where the blat servers are located and what ports to use. See an example of commented out lines <a href="http://example.com/commented-lines">here</a>. Please note the capital "B" in transBlat.</li>
 </ul>
 <pre>
 transBlat yourServer.yourInstitution.edu 17777
 blat yourServer.yourInstitution.edu 17779
 isPcr yourServer.yourInstitution.edu 17779
 </pre>
 <ul>
     <li>You should now be able to load and perform blat and PCR operations on your assembly. For example, a URL such as the following would bring up the blat CGI and have your assembly listed at the bottom of the "Genome:" drop-down menu: <a href="http://genome.ucsc.edu/cgi-bin/hgBlat?hubUrl=http://yourServer.yourInstitution.edu/myHub/hub.txt">http://genome.ucsc.edu/cgi-bin/hgBlat?hubUrl=http://yourServer.yourInstitution.edu/myHub/hub.txt</a>. Also note the separate isPcr line provides the option to use a different gfServer than the blat host if desired.</li>
     <li>Some institutions have firewalls that will prevent the browser from sending multiple inquiries to your blat servers, in which case you may need to request your admins add this IP range as exceptions that are not limited: 128.114.119.* That will cover the U.S. <a href="http://genome.ucsc.edu">genome.ucsc.edu</a> site. In case you may wish the requests to work from our European Mirror <a href="http://genome-euro.ucsc.edu">genome-euro.ucsc.edu</a> site, you would want to include 129.70.40.120 also to the exception list.</li>
 </ul>
 
 <p>Please see more about <a href="http://example.com/configuring-your-blat-gfserver">configuring your blat gfServer</a> to replicate the UCSC Browser's settings, which will also have information about optimizing PCR results. The <a href="http://example.com/source-downloads">Source Downloads</a> page offers access to utilities with pre-compiled binaries such as gfserver found in a blat/ directory for your machine type <a href="http://example.com/here">here</a> and further blat documentation <a href="http://example.com/here">here</a>, and the gfServer usage statement for further options.</p>
-<p>Please also know you can set up gfservers on a <a href="http://example.com/gbibi">GBiB</a> and run it locally. Please see this <a href="http://example.com/gbib-assembly-blat-step-by-step-setup">GBiB assembly blat step-by-step set up</a> page for details.</p>
+<p>Please also know you can set up gfservers on <a href="docker.html">docker</a> and run it locally. 
+
 <p>Note: You can stop your instance of gfServer with a command. For example:</p>
 <pre>
 gfServer stop localhost 17860
 </pre>
 
 <h3>Troubleshooting BLAT servers</h3>
 <p>You can see this error if you have the translatedBlat / nucleotideBlat port numbers the wrong way around:</p>
 <pre>
 Expecting 6 words from server got 2
 </pre>
 <p>The following is an example of an error message when attempting to run a DNA sequence query via the web-based BLAT tool after loading a hub, after starting a gfServer instance (from the same dir as the 2bit file). For example, a command to start an instance of gfServer:</p>
 <pre>
 gfServer start localhost 17779 -stepSize=5 contigsRenamed.2bit &
 </pre>
 <p>Example of a possible error message, from web-based BLAT after attempting a web-based BLAT query:</p>