13e0fcf19a6d71108ecb13289c09de4c1286780c
jnavarr5
  Fri Sep 26 14:27:58 2025 -0700
Fixing broken links reported by the student interns, refs #36072

diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
index 74e2d210dfc..d22d7f638c4 100755
--- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
@@ -64,34 +64,34 @@
   <input type="submit" value="Submit"></p>
 </form> 
 </div> 
 <p> 
 <a href="../../contacts.html">Questions and feedback are welcome</a>.</p>
 
 <!-- ========== What Are Track Hubs? ============================== -->
 <a name="Intro"></a>
 <h2>What Are Track Hubs?</h2> 
 <p>
 Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome 
 Browser (please note that hosting hub files on HTTP tends to work even better than FTP and local 
 hubs can be displayed on <a  href="hubQuickStartAssembly.html#blatGbib" target="_blank">GBiB</a>).  
 Track hubs can be displayed on genomes that UCSC directly supports, or on your own sequence. Hubs 
 are a useful tool for visualizing a large number of genome-wide data sets. For example, a project 
-that has produced several wiggle plots of data can use the hub utility to organize the tracks into 
-composite and super-tracks, making it possible to show the data for a large collection of tissues 
-and experimental conditions in a visually elegant way, similar to how the ENCODE native data tracks 
-are displayed in the browser.</p>
+that has produced several <a href="wiggle.html" target="_blank">wiggle plots</a> of data can use the
+hub utility to organize the tracks into composite and super-tracks, making it possible to show the
+data for a large collection of tissues and experimental conditions in a visually elegant way,
+similar to how the ENCODE native data tracks are displayed in the browser.</p>
 <p>
 The track hub utility allows efficient access to data sets from around the world through the 
 familiar Genome Browser interface. Browser users can display tracks from any public track hub that 
 has been registered with UCSC. Additionally, users can import data from unlisted hubs or can set up,
 display, and share their own track hubs. Genome assemblies that UCSC does not support can be loaded 
 and viewed with associated data.</p>  
 <p>
 The data underlying the tracks and optional sequence in a hub reside on the
 remote server of the data provider rather than at UCSC. Genomic annotations are
 stored in compressed binary indexed files in bigBed, bigBarChart, bigGenePred,
 bigNarrowPeak, bigMethyl, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL,
 hic or VCF format that contain the data at several resolutions. In the case of
 assemblies that UCSC does not support, genomic sequence is stored in the
 efficient twoBit format. When a hub track is displayed in the Genome Browser,
 only the relevant data needed to support the view of the current genomic region
@@ -185,31 +185,31 @@
 <ul>
 <li><a href="http://genome.ucsc.edu/s/ExampleUser/TrackHubSession">
 http://genome.ucsc.edu/s/ExampleUser/TrackHubSession</a></li>
 </ul>
 <p>For additional information, see <a href="hgSessionHelp.html#HowToShare">sharing Saved Sessions
 </a> and
 <a href="hgSessionHelp.html#Create">
 backing up custom data</a>.</p>
 
 
 
 
 <a name="hubUrl"></a>
 <h3>Creating a URL for a Track Hub</h3>
 <p>Hubs can be loaded into the URL using the <code>hubUrl=</code> parameter. This parameter
-takes input similar to the <a href="../cgi-bin/hgHubConnect#unlistedHubs">track hub input box</a>.
+takes input similar to the <a href="/cgi-bin/hgHubConnect#unlistedHubs">track hub input box</a>.
 Native UCSC supported genomes can be loaded into the URL using the <code>db=</code> parameter while
 non-natively supported genomes such as assembly hubs or GenArk hubs use the <code>genome=</code>
 parameter. URL parameters can be combined by using <code>&amp;</code>.
 </p>
 <p>The following example links to the hg19 genome database and an example track hub using the <code>db=</code> and the <code>hubUrl=</code> parameters:</p>
 <pre><a href=../../cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt>http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt</a></pre>
 
 <p>Track hubs' track visibility can also be changed from the URL parameters. As an example, the
 following link specifies:
 <ul>
 <li> the genome database (db=hg38)</li>
 <li> loads a track hub (hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt)</li>
 <li> hides all tracks (hideTracks=1)</li>
 <li> hides the subtrack kids of a particular track (gtexRnaSignalMaleYoung_hideKids=1)</li>
 <li> sets a specific subtrack to be displayed (gtexRnaSignalSRR1311243=full)</li>
@@ -276,31 +276,31 @@
 https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt
 </pre>
 <p>
 The combination of the three hubs allows the creation of the following URL that can load the
 three hubs on the Genome Browser.
 </p>
 <pre>
 <a href="/cgi-bin/hgTracks?db=hg38&hubUrl=https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&hubUrl=https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt" target="_blank">https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https://storage.googleapis.com/gcp.wenglab.org/hubs/dna20/hub.txt&hubUrl=http://expdata.cmmt.ubc.ca/JASPAR/UCSC_tracks/hub.txt&hubUrl=https://remap.univ-amu.fr/storage/public/hubReMap2022/hub.txt</a></pre>
 
 <h3>Creating a URL for an Assembly Hub</h3>
 
 <p>
 The following example links to an assembly hub using the <code>hubUrl=</code> and
 <code>genome=</code> parameters where in the example, <code>genome=araTha1</code>, is the assembly
 name set for <code>genome</code> in the genomes.txt file. URL parameters can be combined by using <code>&amp;</code>.</p>
-<pre><a href=../cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt>https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></pre>
+<pre><a href=/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt>https://genome.ucsc.edu/cgi-bin/hgTracks?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</a></pre>
 </p>
 <h6>Additional hub connection parameters</h6>
 <ul>
 <li id="hubClear"><code>hubClear=</code>connects the hub and disconnects other hubs that are in the same directory</li>
 <li id=hgHubConnect><code>hgHubConnect</code>Replacing <code>hgTracks</code> with this parameter connects the hub and redirects the link to the
 <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#unlistedHubs" target="_blank">Track Data Hubs</a> page</li>
 <li id="hgHub_do_firstDb"><code>hgHub_do_firstDb=1</code>
 uses the first database in genomes.txt</li>
 <li id="hgHub_do_redirect"><code>hgHub_do_redirect=on</code>
 redirects the attached hub to the Gateway page</li>
 </ul>
 <h6>Redirecting the URL to the Gateway page</h6>
 <p>
 The following example link connects the hub and redirects the link to the Gateway page to display
 the hub's description html page, which is defined in the genomes.txt by the <code>htmlPath</code>