03e853f795d04dbdd939c9fbef0186cc339bafde
gperez2
  Mon Jan 25 18:02:10 2021 -0800
Adding example on how to make gfidx files and updating the doc, refs #26658

diff --git src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
index 95ac977..999ae48 100755
--- src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
+++ src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
@@ -135,41 +135,50 @@
 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 myGenome.untrans.gfidx myGenome.2bit
+gfServer index -trans myGenome.trans.gfidx myGenome.2bit
+</pre>
+</p>
+
 <p>
-for files names in the form:
+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 for more deeply nest directory, for instance, for instance following the NCBI
+For for more deeply nest directory, for instance, the 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>