be3d8b28bd4ee8c75dec5878957b7650ed8f066b dschmelt Wed Nov 4 12:31:16 2020 -0800 Emphasizing sessions for sharing hubs #26462 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 436eff7..0d18b69 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -139,55 +139,72 @@ below the browser image and can be <a href="hgTracksHelp.html#FineTuning">configured</a> just like native browser tracks. Exercise caution when viewing a wide region that requires the Genome Browser to display a large number of track features: the browser display may time out. </p> <a name="unlistedHubs"></a> <h3>Unlisted hubs (located in the <a href="../../cgi-bin/hgHubConnect#unlistedHubs">My Hubs</a> tab)</h3> <p>In addition to the Public Hubs listed, it is possible to load your own track hub or one created by a colleague. To add an unlisted hub, open the Track Hubs page and click the <a href="../../cgi-bin/hgHubConnect#unlistedHubs"> My Hubs</a> tab. To import a new hub, type or paste its URL into the text box, then click the Add Hub button. If successful, your track hub will appear on that page.</p> <p> -It is also possible to add or share a track hub by directly by URL. If you add -<strong>hubUrl=[URL]</strong> to your hgTracks URL line, it will add the hub directly into the -browser:</p> -<ul> -<li><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt"> -http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt</a></li></ul> -<p> -If you are adding an assembly hub with multiple genomes, you can link directly to hgGateway, -the assembly selection page and a particular genome:</p> -<ul> -<li><a href="../../cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt"> -http://genome.ucsc.edu/cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt</a></li></ul> -<p> Tracks accessed through a hub can be used in Genome Browser <a href="hgSessionHelp.html">sessions</a> and <a href="hgTracksHelp.html#CustomTracks">custom tracks</a> in the same manner as other tracks. The data underlying data hub tracks can be viewed, manipulated, and downloaded using the <a href="../../cgi-bin/hgTables">UCSC Table Browser</a>. To remove a track hub from your Genome Browser display, click the "Disconnect" button on the Track Hubs page.</p> <p> For confidential or private data, please note that unlisted hubs are not secure. The URL helps to hide the location of the data; it is a simple barrier of obscurity. Please also know that hubs can be loaded from local directories when using <a href="hubQuickStartAssembly.html#blatGbib">GBiB</a>.</p> +<a name="Sharing"></a> +<h3>Sharing Track Hubs</h3> +<p>When sharing track hubs on a single assembly from manuscripts, publications, +or on research websites, we recommend using a session to link to +the Genome Browser view attached to that particular track hub. This has the advantage +of being able to save and share configuration settings made on other, native browser tracks. +The process for generating a session link to share a track hub for a manuscript is to +make the hub on your web-accessible server, attach the hub to the Genome Browser, configure +browser position and related tracks, then <a href="../../cgi-bin/hgSession"> +save your named session</a> and share the +session link. Your session links will be in the following format with +your chosen username and session name:</p> +<ul> +<li><a href="http://genome.ucsc.edu/s/ExampleUser/TrackHubSession"> +http://genome.ucsc.edu/s/ExampleUser/TrackHubSession</a></li> +</ul> +<p> +It is also possible to add or share a track hub directly by URL. If you add +<strong>hubUrl=[URL]</strong> to your hgTracks URL line, it will add the hub directly into the +browser:</p> +<ul> +<li><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt"> +http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt</a></li></ul> +<p> +If you are adding an assembly hub with multiple genomes, you can link directly to hgGateway, +the assembly selection page and a particular genome:</p> +<ul> +<li><a href="../../cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt"> +http://genome.ucsc.edu/cgi-bin/hgGateway?genome=GCF_000699105.1&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/birds/hub.txt</a></li></ul> + <!-- ========== Setting Up Your Own Track Hub ============================== --> <a name="Setup"></a> <h2>Setting up your own Track Hub</h2> <p> This section provides a step-by-step description of the process used to set up a track hub on your own server.</p> <p> To create your own hub you will need:</p> <ul> <li> one or more data sets formatted in one of the compressed binary index formats supported by the Genome Browser: bigBed, bigBarChart, bigGenePred, bigNarrowPeak, bigPsl, bigChain, bigInteract, bigMaf, bigWig, BAM, CRAM, HAL, hic or VCF</li> <li> a set of text files that specify properties for the track hub and for each of the data tracks