a74c645505a135d5c1e923afe477cdeb9c15bded
markd
  Wed Jul 8 22:27:42 2020 -0700
added including multiple container directoies in genome dir path to gfServer

diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
index 772400a..140d7c3 100755
--- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
+++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
@@ -106,37 +106,82 @@
 
 <!-- ========= assembly blat ============================== -->
 
 <a name="blat"></a>
 <h2>Starting Blat for an Assembly Hub</h2>
 <p>
 From the location of yourAssembly.2bit file,
 <code>http://yourURL/yourAssembly/yourAssembly.2bit</code>, you can start two gfServers, specifying 
 a port for the assembly hub to access amino acid sequence, <code>17777 -trans</code>, or DNA 
 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 two lines in the stanza 
 referring to yourAssembly, that would have matching port numbers:</p>
-<pre><code>transBlat yourLab.yourInstitution.edu 17777
-blat yourLab.yourInstitution.edu 17779 </code></pre>
+<pre>
+   transBlat yourLab.yourInstitution.edu 17777
+   blat yourLab.yourInstitution.edu 17779
+</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.
+<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 directory contain the
+<code>2bit</code> and <code>gfidx</code> files.   The final genome
+directory and base name of the data files must be the same as the
+genome name.
+<p>
+For example:
+<pre>
+   transBlat yourLab.yourInstitution.edu 4096 dynamic myGenome
+   blat yourLab.yourInstitution.edu 4096 dynamic myGenome
+</pre>
+</p>
+<p>
+for files store in the form:
+<pre>
+    $rootdir/myGenome/myGenome.2bit
+    $rootdir/myGenome/myGenome.untrans.gfidx
+    $rootdir/myGenome/myGenome.trans.gfidx
+</pre>
+</p>
+
 <p>
-An addition argument of the string <code>dynamic</code> to the <code>blat</code>
-or <code>transBlat</code> specification indicates that the BLAT server is dynamic and
-started by <code>xinetd</code>.  See <code>gfServer</code> documentation for the details
-of configuring a dynamic BLAT server.
+For for more deeply nest directory, for instance, for instance following the 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>