63c0f6234dbcc0c3fdc9bc2d0e673c8313bd6443 mspeir Sun Sep 27 11:57:25 2026 -0700 two minor fixes from automated CR, #37641 diff --git src/hg/htdocs/goldenPath/help/assemblyHubHelp.html src/hg/htdocs/goldenPath/help/assemblyHubHelp.html index d854232b295..5444e08261a 100755 --- src/hg/htdocs/goldenPath/help/assemblyHubHelp.html +++ src/hg/htdocs/goldenPath/help/assemblyHubHelp.html @@ -416,31 +416,31 @@ longLabel Variant calls over hg19 region type vcfTabix visibility pack bigDataUrl http://myServer.com/data/example.vcf.gz </pre> <ul> <li>The <strong>hub</strong> stanza with the <strong>useOneFile on</strong> setting replaces <code>hub.txt</code>.</li> <li>The <strong>genome</strong> line replaces <code>genomes.txt</code>.</li> <li>The <strong>track</strong> stanzas replace <code>trackDb.txt</code>.</li> </ul> <p> If your hub requires a reference genome sequence, you can still provide a <code>.2bit</code> file with <code>twoBitPath</code>. Grouping (previously in -<a href="#groupsTxt">groups.txt</a>). can also be integrated here if needed. +<a href="#groupsTxt">groups.txt</a>) can also be integrated here if needed. </p> <p> Once hosted on a server, the single configuration file (and associated data files such as <code>.bigWig</code>, <code>.vcf.gz</code>, <code>.2bit</code>) can be loaded into the UCSC Genome Browser via the <b>Connected Hubs</b> tab of the <a href="/cgi-bin/hgHubConnect" target="_blank">Track Data Hubs</a> page.</p> <a id="buildingTracks"></a> <h2>Building Tracks</h2> <p>Tracks are defined in the <strong>trackDb.txt</strong> file, where each stanza specifies how tracks are displayed (shortLabel, longLabel, color, visibility), along with other information such as the group the track belongs to (referencing <a href="#groupsTxt">groups.txt</a>) and whether additional HTML should be displayed when a user clicks into the track or a track item:</p> <pre> @@ -770,31 +770,30 @@ IP/port configuration is incorrect.<br> The <code>genomes.txt</code> file should also be checked to confirm that the BLAT line matches the correct IP and port. For example: <pre>blat 132.249.245.79 17777</pre> Instead of: <pre>blat localhost 17777</pre></li> <li><b>Check gfServer status</b><br> Request status directly from <code>gfServer</code>: <pre>gfServer status yourLocation yourPort</pre> For example: <pre>gfServer status 132.249.245.79 17777</pre> Sample output might look like: <pre> version 39x1 serverType static -version 39x1 type nucleotide host localhost port 17777 tileSize 11 stepSize 5 minMatch 2 pcr requests 0 blat requests 0 bases 0 misses 0 noSig 0 trimmed 0 warnings 0 </pre></li> <li><b>Test with gfClient</b><br>