95030f73f067d8e8f9221a09c1811784607e4e72
markd
  Fri Jul 10 17:51:29 2020 -0700
split  dynamic server genomeDataPrefix into genome and genomeDataDir.  More verbose, but clearer

diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
index 140d7c3..f3a79ce 100755
--- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
+++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
@@ -119,47 +119,50 @@
 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>
    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.
+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 myGenome
-   blat yourLab.yourInstitution.edu 4096 dynamic myGenome
+   transBlat yourLab.yourInstitution.edu 4096 dynamic jillLab
+   blat yourLab.yourInstitution.edu 4096 dynamic jillLab
 </pre>
 </p>
 <p>
-for files store in the form:
+for files names in the form:
 <pre>
-    $rootdir/myGenome/myGenome.2bit
-    $rootdir/myGenome/myGenome.untrans.gfidx
-    $rootdir/myGenome/myGenome.trans.gfidx
+    $rootdir/jillLab/myGenome.2bit
+    $rootdir/jillLab/myGenome.untrans.gfidx
+    $rootdir/jillLab/myGenome.trans.gfidx
 </pre>
 </p>
 
 <p>
 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