bbabbd5d2566d47d923d51dbe350634783455999
mspeir
  Sun Oct 26 12:14:52 2025 -0700
change soe to gi, refs #35031

diff --git src/hg/htdocs/goldenPath/help/trackDbIndexBb.html src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
index 9cdde9b8aeb..27ea2c519a7 100755
--- src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
+++ src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
@@ -18,61 +18,61 @@
 underlying bigBed files, using the <code>trackDbIndexBb</code> utility. This utility
 creates multibed/index files containing the coordinates where the tracks intersect,
 expediting data lookup. There are two instances in which these files are helpful or required:</p>
 <ul>
 <li><b>(helpful)</b> In large composites (dozens or hundreds of tracks), especially when subtrack
 data are sparse, the index files will provide a substantial performance improvement.</li>
 <li><b>(required)</b> For building track associations. An example of this is when it is desired
 to display peak and signal tracks together. Because <code>hideEmptySubtracks</code> works
 only on bigBed tracks (peaks), associated tracks (such as bigWig signals) can be designated
 to be displayed alongside the bigBeds with data.</li>
 </ul>
 
 <p>
 To build the index files, first download the <code>trackDbIndexBb</code> utility. 
 For more information on downloading our command line utilities, see these 
-<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">instructions</a>.</p>
+<a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">instructions</a>.</p>
 <p>
 There are three other programs needed to run <code>trackDbIndexBb</code>. Two of them,
 <code>bedToBigBed</code> and <code>bigBedToBed</code>, can be found
-in the same <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">
+in the same <a href="http://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads">
 downloads directory</a>.
 The final dependency, <b>bedtools</b>, can be found on the <a target="_blank" 
 href="https://bedtools.readthedocs.io/en/latest/">bedtools site</a>.</p>
 
 <h2>Parameters</h2>
 <p>
 Kent utilities can be run with no parameters to display a usage message. 
 Additionally, <code>trackDbIndexBb</code> can be passed the
 <code>-	h</code> flag to display a more verbose help message.</p>
 <pre>
 ./trackDbIndexBb
 ./trackDbIndexBb -h
 </pre>
 <p> 
 Below is a short description of the parameters:</p>
 <ul>
 <li><b>trackName</b> | The name of the composite containing the bigBed tracks
 to be indexed. Higher-level composite names may be used to build track associations.
 This means that all tracks in the hierarchy <em>below</em> trackName will be searched 
 for indexing and associations.</li>
 <li><b>raFile</b> | The location of the trackDb.ra file containing the bigDataUrls
 of the bigBeds to be indexed.</li>
 <li><b>chromSizes</b> | Location of the chrom.sizes file. This file contains the names
 and sizes of the chromosomes for the working assembly. This can be generated from the 2bit genome, 
 downloaded from the respective assembly on our <a target="_blank" 
-href="http://hgdownload.soe.ucsc.edu/downloads.html">download server</a>, or fetched using the 
+href="http://hgdownload.gi.ucsc.edu/downloads.html">download server</a>, or fetched using the 
 <code>fetchChromSizes</code> utility found in the same directory as <code>trackDbIndexBb</code>.
 </li>
 <li><b>-o --out</b> | (Optional) Path to the output directory where the resulting files will 
 be placed. Defaults to current directory.</li>
 <li><b>-p --pathTools</b> | (Optional) Location where the dependent programs can be found. 
 Will automatically check current directory and user's path. <code>trackDbIndexBb</code> 
 has three dependencies listed above. Note that bedtools must be downloaded from an 
 external group.</li>
 <li><b>-n --noDelete</b> | (Optional) Keep intermediary multiBed file.</li>
 <li><b>-m --metaDataVar</b> | (Optional) Used only when building track associations. The variable
 designated here will be a trackDb variable which can be used to associate tracks. Default value is
 <em>subGroups</em>, though <em>metaData</em> is also commonly used. See example below for more 
 information.</li>
 <li><b>-s --subGroupRemove</b> | (Optional) Used only when building track associations. In 
 conjunction with <b>--metaDataVar</b>, this variable is used to build track associations. The