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

diff --git src/hg/htdocs/goldenPath/help/assemblyHubHelp.html src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
index 1dbe7943eaf..68c8e91cd4b 100755
--- src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
+++ src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
@@ -8,31 +8,31 @@
 <h1>Assembly Hub User Guide</strong></h1>
 
 <a id="overview"></a>
 <h2>Overview</h2>
 <p>
 An Assembly Data Hub is a set of Internet-accessible data files that define the reference sequence
 to be used for a browser instance, as well as all the data files that define the annotation for
 that sequence. Assembly Data Hubs allow researchers to use the UCSC Genome Browser to view their
 own sequences with associated annotation, without the requirement that UCSC support a browser on that sequence.
 </p>
 
 <p>
 <b>Note</b>: if you are working with a genome that has already been submitted
 to the <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/">NCBI Assembly</a> system, it may
 already be available in the <a href="https://genome.ucsc.edu">UCSC Genome Browser</a>.
-Please check the <a href="https://hgdownload.soe.ucsc.edu/hubs/">GenArk Assembly Hub</a> collection
+Please check the <a href="https://hgdownload.gi.ucsc.edu/hubs/">GenArk Assembly Hub</a> collection
 to see if your genome of interest is already available. If it is not listed there, you can use the
 <a href="/assemblyRequest">UCSC Assembly Request</a> page to request that the genome assembly be
 added.</p>
 
 
 <h2>Contents</h2>
 <h6><a href="#webServer">Web Server</a></h6>
 <h6><a href="#hubTxt">Assembly Hub Components</a></h6>
     <ul style="margin-left: 20px;">
         <li><a href="#hubTxt">hub.txt</a></li>
 	<li><a href="#genomesTxt">genomes.txt</a></li>
 	<li><a href="#twoBitFile">2bit File</a></li>
 	<li><a href="#chromAlias">chromAlias</a></li>
         <li><a href="#groupsTxt">groups.txt</a></li>
 	<li><a href="#singleFileHub">Single-File Track Hub</a></li> 
@@ -163,31 +163,31 @@
     <li><strong>htmlPath</strong> points to the HTML file with assembly information. The HTML file
 	    is displayed on the Gateway page.</li>
     <li><strong>transBlat</strong>, <strong>blat</strong>, and <strong>isPcr</strong> configure
 	    different gfServer instances for amino acid searches, BLAT alignments, and PCR.
 	    <a href="#configuringAssemblyHubs"> More here.</a></li>
 </ul>
 <p><b>Note</b>: it is strongly recommended that each genome stanza includes <em>defaultPos</em>,
 <em>scientificName</em>, <em>organism</em>, <em>description</em>, so that the hub loads with
 meaningful defaults and can be more easily searched from the Gateway page.</p>
 
 <a id="twoBitFile"></a>
 <h3>2bit File</h3>
 <p>
 The <strong>.2bit</strong> file is constructed from the FASTA sequence for the assembly using the
 <strong>faToTwoBit</strong> <em>kent</em> program (available from the
-<a href="https://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">downloads</a> page).</p>
+<a href="https://hgdownload.gi.ucsc.edu/admin/exe/" target="_blank">downloads</a> page).</p>
 <p>Example:</p>
 <pre>
 faToTwoBit ricCom1.fa ricCom1.2bit
 </pre>
 <p>
 Use <strong>twoBitInfo</strong> to verify sequences and create a <strong>chrom.sizes</strong> file,
 which is not used in the hub itself but is helpful for constructing <strong>big*</strong> files:
 </p>
 <pre>
 twoBitInfo ricCom1.2bit stdout | sort -k2rn &gt; ricCom1.chrom.sizes
 </pre>
 <p>
 The <em>.2bit</em> file can also be hosted at a URL:</p>
 <pre>
 twoBitInfo -udcDir=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubPlants/cshl2013/ricCom1/ricCom1.2bit stdout | sort -k2nr &gt; ricCom1.chrom.sizes