e70cfc3b3ff31a9876df98f242162f60f839a7e9 brianlee Wed Jun 8 08:05:42 2022 -0700 Add doc back for hubClear (removed by 39e3bc63) & other hub loading parameters #29562 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index 5ccf205..b412092 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -234,30 +234,70 @@ <p> To link to an assembly hub and display data on a non-natively supported genome, the same parameters apply. To specify the intended genome assembly, instead of using <code>db=</code>, you must use <code>genome=araTha1</code>, where araTha1 is the assembly name set by your genomes.txt file in the line <code>genome araTha1</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> <p> To see the files behind that assembly hub, please visit the <a href="../goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/"> hub's directory</a>. For more information on assembly hubs in general, please see the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target ="_blank">assembly hub wiki</a>, the <a href="../goldenPath/help/hgTrackHubHelp.html">track hub user guide</a>, or the <a href=../goldenPath/help/hubQuickStartAssembly.html>quick start guide to assembly hubs</a>. </p> +<h6 id="hubClear">Use <code>hubClear=</code> to remove hubs at the same location</h6> +<p> +Another feature one can use in place of <code>hubUrl=</code> is +<code>hubClear=</code>, which will load a hub while simultaneously disconnecting +or clearing, hubs located at the same location. For example, adding +<code>hubClear=http://university.edu/lab/folder/hub10.txt</code> would connect the +referenced hub10.txt while simultaneously disconnecting any hubs that might be +displayed from the same <code>http://university.edu/lab/folder/</code> directory +(for example, hub1.txt, hub2.txt, etc.). This feature can be useful for dynamically +generated hubs that might collect in the browser otherwise. +</p> +<h6>Additional hub connection parameters</h6> +<p> +Alongside <code>hubUrl</code> and <code>hubClear</code> there are other parameters +you can add to either if you wished, for instance, to attach an assembly hub and +display the Gateway page, while also sharing your contact email.</p> +<ul> +<li id="hgHubConnect.remakeTrackHub"><code>hgHubConnect.remakeTrackHub=on</code> +acts to connect when pointed to /hgHubConnect</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> +<p> +By pointing the URL to <code>/cgi-bin/hgHubConnect</code> the hub would be connected to +and then redirect to the Gateway page to display the page in <code>genomes.txt</code> defined +by the <code>htmlPath ../newOrg.html</code> line. Here is an example:</p> +<pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt" +target="_blank">http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=1&<strong>hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</strong></a></code> +</pre> +<h6 id="genome">Use <code>genome=</code> for assembly hubs</h6> +<p> +There is also another way to connect an assembly hub using the <code>genome=</code> to arrive at +the Gateway page if you know the genome in <code>genomes.txt</code> that you wish to display. +For instance, the below link skips the redirection step, where your +<code>hub.txt</code> contact email gets displayed, by pointing to the +<code>/cgi-bin/hgGateway</code> page:</p> +<pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt" +target="_blank"><strong>http://genome.ucsc.edu/cgi-bin/hgGateway?genome=araTha1&hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt</strong></a> </code></pre> <a name="trackHubLoading"></a> <h3>Attaching a track hub to an assembly hub</h3> <h6>How do I attach a track hub to an assembly hub?</h6> <p> It is possible to attach a track hub to an assembly hub via the URL using a combination of the <code>hubUrl=</code> and <code>genome=</code> URL parameters. For example, using the following assembly hub and track hub: </p> <pre> <b>Arabidopsis thaliana assembly hub</b> https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubPlants/cshl2013/hub.txt </pre> <pre> <b>ReMap2020 Reg. Atlas track hub</b>