fb4ffcb9317cff2f672d44d692e1433288728c25 mspeir Wed Mar 11 08:59:36 2026 -0700 Tweaks based on automated CR, refs #37221 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html index b389f878c9b..b157887f9c1 100755 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html @@ -45,58 +45,58 @@ <!--Content Tables--> <!--outer table is for border purposes--> <div class="contentBorder"> <div class="lightBlueBar"> <div class="lightBlueBarTitle"> Track Database Definition</div> </div> <!-- Finally to the content --> <div class="borderGuard"> <DIV class="trackDbHub_intro"> <H1>Hub Track Database Definition (<SPAN id="trackDbHub_version">v3</SPAN>)</H1> <H2>How to declare Dataset Display Settings in Genome Browser Hubs</H2> <p> This page describes all of the settings one might use in creating a -<a href="/goldenPath/help/hgTrackHubHelp.html">track or assembly hub</a>. +<a href="/goldenPath/help/hgTrackHubHelp.html" target="_blank">track or assembly hub</a>. Hubs display your own data in the Genome Browser by hosting your files on a web server and connecting them with a simple text configuration file, giving you more control and permanence than custom tracks. This initial section touches on the files and settings needed in creating a hub before providing a listing of settings separated by track type.</p> <p> For those new to creating hubs: Our <a href="/docs/hubs/hubBasics.html" -target"_blank">Hub Basics</a> page provides a simple introduction to creating hubs.</p> +target="_blank">Hub Basics</a> page provides a simple introduction to creating hubs.</p> <p> For returning readers: We keep a <a href="changes.html">list of changes</a> to the trackDb specification below.</p> <h3 id="hub_txt">Start with a hub.txt</h3> <p> All hubs must include a top-level hub.txt file. This file contains general settings that identify your hub in our internal databases and in the Genome Browser interface. The URL to the hub.txt is used to load your hub. Our <a href="/docs/hubs/hubBasics.html" -target"_blank">Hub Basics</a> describes how to create a hub.txt. +target="_blank">Hub Basics</a> describes how to create a hub.txt. A full listing of hub.txt settings can be found in the <a HREF="#hubGeneral">General hub configuration settings</a> section below.</p> <p> If your hub contains tracks on a single genome assembly, then you can put all of the hub, genome, and track configuration settings into a single file with -<code><a href="hgTracksHelp.html#UseOneFile" target="_blank">useOneFile</a></code>. +<code><a href="hgTracksHelp.html#UseOneFile" target="_blank">useOneFile</a></code>.</p> <h3 id="genomes_txt">Defining your hub's genomes</h3> <p> A genomes.txt is only necessary if you are <b>NOT</b> using the <code>useOneFile</code> setting as described <a href="#useOneFile">below</a>. When using <code>useOneFile</code>, one only needs to include the <code><a href="#genome">genome</a></code> line. This line will reference a UCSC assembly name (e.g. hg38) or a GenBank assembly available through our <a href="https://hgdownload.gi.ucsc.edu/hubs" target="_blank">GenArk archive</a> beginning with GCF or GCA (e.g. GCF_000891275.1). <p> If your hub contains tracks for more than one genome, you will need to define a <a target="_blank" href="../hgTrackHubHelp.html#genomes.txt"><code>genomes.txt</code></a>. A full listing of