87510802d69dfeccd7ae00b02cf66fe8074f0a70
max
  Mon Jul 19 03:59:13 2021 -0700
documenting local-only assemblies in gbib, refs #27865

diff --git src/hg/htdocs/goldenPath/help/gbib.html src/hg/htdocs/goldenPath/help/gbib.html
index 5839b6a..209ad5c 100755
--- src/hg/htdocs/goldenPath/help/gbib.html
+++ src/hg/htdocs/goldenPath/help/gbib.html
@@ -529,30 +529,49 @@
 "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM1186795&format=file&file=GSM1186795%5FDZ012%5FTRA1%5FN2L3%5Ftr27%5Fce10%5FBTm1x200n%2Ebw" -O GSM1186795.bw </code></pre>
 <p>
 The file can then be found in the GBiB's 
 <a href="http://127.0.0.1:1234/folders/"><code>http://127.0.0.1:1234/folders/</code></a> location, 
 or loaded with a direct link to the files location:</p> 
 
 <pre><code><a href="http://127.0.0.1:1234/cgi-bin/hgTracks?db=hg19&hgt.customText=http://127.0.0.1:1234/folders/GSM1186795.bw&position=chrM" 
 target="_blank">http://127.0.0.1:1234/cgi-bin/hgTracks?db=hg19&hgt.customText=<strong>http://127.0.0.1:1234/folders/GSM1186795.bw</strong>&position=chrM</a></code></pre>
 <p>
 (NOTE: In this above example, the <strong>ftp location</strong> now has byte-range requests 
 supported so the <strong>GEO ftp link</strong> can be loaded on the browser).</p>
 
 <a name="CustomizingGbib"></a>
 <h2>Customizing your GBiB</h2>
 
+<h3>Allowing local-only assemblies</h3>
+<p>By modifying the MySQL table hgcentral.dbDb one can add a genome directly to
+the UCSC Genome Browser, as documented in <a
+    href="mirrorManual.html#adding-a-new-custom-non-ucsc-genome-to-the-browser">
+our manual mirror instructions</a>. We discourage this, as assembly hubs,
+especially in combination with a "default cart" (see below) are much easier to
+setup. However, if you have an existing local genome browser installation with
+genomes that only exist only there, in order to combine its "remote access" mode with
+a local-only genome, the local genome has to be declared in hg.conf, or for GBIB, 
+rather /usr/local/apache/cgi-bin/hg.conf.local. The statement is
+<pre>slow-db.excludeDbs=assemblyName1,assemblyName2</pre>
+For example, if you have two local-only assemblies defined in dbDb with the
+names homSap1 and homSap2, the
+statement <pre>slow-db.excludeDbs=homSap1,homSap2</pre> will instruct the browser to 
+never try to connect
+to the UCSC Public MySQL server for these two assemblies, avoiding error messages
+and significantly speeding up the display.
+</p>
+
 <!--
 <a name="Fonts"></a>
 <h3>Enabling additional font styles</h3>
 <p>
 To enable the use of additional fonts in the tracks display, the following lines
 need to be need to be added to the <code>hg.conf</code> file:</p>
 <pre>
 freeType=on
 freeTypeDir=/usr/share/fonts/type1/gsfonts
 </pre>
 <p>
 The file can be found in the following location:</p>
 <pre>
 /usr/local/apache/cgi-bin/hg.conf
 </pre>