71a2c73633337ab11c6344fee8c077e13daf815b
markd
  Tue Feb 2 12:03:42 2021 -0800
move most doc on setting up dynamic blat servers to the wiki

diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
index 41c25c8..91f4c5f 100755
--- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
+++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
@@ -115,88 +115,36 @@
 sequence, <code>17779</code>, in this example:</p>
 <pre><code>gfServer start localhost 17777 -trans -mask yourAssembly.2bit &
 gfServer start localhost 17779 -stepSize=5 yourAssembly.2bit &</code></pre>
 <p>
 Then you can edit the genomes.txt file of your assembly hub to include three lines in the stanza 
 referring to yourAssembly, that would have matching port numbers:</p>
 <pre>
    transBlat yourLab.yourInstitution.edu 17777
    blat yourLab.yourInstitution.edu 17779
    isPcr yourLab.yourInstitution.edu 17779 </code></pre>
 </pre>
 <p>
 The assembly hub can be configured to talk to a dynamic BLAT server that loads
 a pre-built index when started by an <code>xinetd</code> super-server.  This
 allows genomes to have a blat server without needing it to be resident in
-memory at all times.
+memory at all times.  See
+<a href="http://genomewiki.ucsc.edu/index.php/Running_your_own_gfServer">Running your own gfServer</a>
+and
+<a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Adding_BLAT_servers">Adding BLAT servers</a>
+for details on how to setup dynamic BLAT servers
 <p>
-</p>
-A dynamic BLAT server is specified with the <code>dynamic</code> argument to
-the <code>blat</code> or <code>transBlat</code> specification, followed by
-the <code>gfServer</code> dynamic root-relative path of the directory
-containing the <code>2bit</code> and <code>gfidx</code> files, named in the form
-<ul>
-  <li><code><em>myGenome</em>.2bit</code> - two-bit format genomic sequence
-  <li><code><em>myGenome</em>.untrans.gfidx</code> - untranslated index, built by <code>gfServer index</code>
-  <li><code><em>myGenome</em>.trans.gfidx</code> - translated index, built by <code>gfServer -trans index</code>
-</ul>
-<p>
-For example:
-<pre>
-   transBlat yourLab.yourInstitution.edu 4096 dynamic jillLab
-   blat yourLab.yourInstitution.edu 4096 dynamic jillLab
-   isPcr yourLab.yourInstitution.edu 4096 dynamic jillLab
-</pre>
-</p>
-
-<p>
-The following commands are an example on how to make the gfidx files:
-<pre>
-gfServer index -stepSize=5 myGenome.untrans.gfidx myGenome.2bit
-gfServer index -trans myGenome.trans.gfidx myGenome.2bit
-</pre>
-</p>
-
-<p>
-The files names in the form:
-<pre>
-    $rootdir/jillLab/myGenome.2bit
-    $rootdir/jillLab/myGenome.untrans.gfidx
-    $rootdir/jillLab/myGenome.trans.gfidx
-</pre>
-</p>
-
-<p>
-For a more deeply nest directory, for instance, the following NCBI
-convention:
-<pre>
-   transBlat yourLab.yourInstitution.edu 4096 dynamic GCF/000/181/335/GCF_000181335.3
-   blat yourLab.yourInstitution.edu 4096 dynamic GCF/000/181/335/GCF_000181335.3
-</pre>
-</p>
-<p>
-will reference these genome files:
-<pre>
-    $rootdir/GCF/000/181/335/GCF_000181335.3/GCF_000181335.3.2bit
-    $rootdir/GCF/000/181/335/GCF_000181335.3/GCF_000181335.3.untrans.gfidx
-    $rootdir/GCF/000/181/335/GCF_000181335.3/GCF_000181335.3.trans.gfidx
-</pre>
-</p>
-
-See <code>gfServer</code> documentation for the details
-of configuring a dynamic BLAT server and generating indexes.
-  
 See an example genomes.txt with commented out lines 
 <a href="http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/genomes.txt"
 target="_blank">here</a>, and please note the uppercase &quot;B&quot; in transBlat. For more 
 information, see the &quot;Adding BLAT servers&quot; section of the 
 <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Adding_BLAT_servers" 
 target="_blank">Assembly Hub Wiki</a>. The 
 <a href="http://hgdownload.soe.ucsc.edu/downloads.html#source_downloads" target="_blank">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://hgdownload.soe.ucsc.edu/admin/exe/" 
 target="_blank">here</a> and further <a href="blatSpec.html" target="_blank">blat documentation 
 here</a>. Please note that because the <code>-mask</code> option in the above <code>17777 
 -trans</code> gfServer option will mask all lower-case sequence from being matched, you may not 
 wish to include it. See the above blat links and gfServer usage statement for more information.</p>
 <p>
 If you have trouble connecting your blat servers with the browser or if the browser cannot access