06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index b7ca375..f4caf49 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -1,35 +1,35 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Track Hubs" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Using UCSC Genome Browser Track Hubs</strong></h1> <h2>Contents</h2> <h6><a href="#Intro">What Are Track Hubs?</a></h6> <h6><a href="#Assembly">What Are Assembly Hubs?</a></h6> -<h6><a href="#View">Viewing Track Hubs in the browser</a></h6> -<h6><a href="#Setup">Setting up your own Track Hub</a></h6> -<h6><a href="#Debug">Debugging and updating Track Hubs</a></h6> -<h6><a href="#Search">Setting up track item search</a></h6> -<h6><a href="#Session">Displaying Track Hubs by URL and in sessions</a></h6> +<h6><a href="#View">Viewing Track Hubs</a></h6> +<h6><a href="#Sharing">Sharing Track Hubs</a></h6> +<h6><a href="#Setup">Setting up a Track Hub</a></h6> +<h6><a href="#Debug">Debugging Track Hubs</a></h6> +<h6><a href="#Search">Setting up item search</a></h6> <h6><a href="#Register">Registering a Track Hub with UCSC</a></h6> -<h6><a href="#Compatibility">Testing hub compatibility between genome browsers</a></h6> +<h6><a href="#Compatibility">Checking Hub settings and compatibility</a></h6> <h6><a href="#Hosting">Where to host your data</a></h6> <hr> <p> <strong>Additional resources</strong></p> <ul> <li>Raney BJ, et al. <a href="https://doi.org/10.1093/bioinformatics/btt637" target="_blank">Track Data Hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser</a>. <em>Bioinformatics</em>. 2014 Apr 1;30(7):1003-5. <li> <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hubs Wiki</a></li> <li> <a href="trackDb/trackDbHub.html" target="_blank">Track Database Definition Document</a> (Reference guide for trackDb parameter definitions)</li> <li> @@ -112,88 +112,105 @@ <a name="Assembly"></a> <h2>What Are Assembly Hubs?</h2> <p> Assembly Data Hubs extend the functionality of Track Data Hubs to assemblies that are not hosted natively on the Browser. Assembly Data Hubs were developed to address the increasing need for researchers to annotate sequence for which UCSC does not provide an annotation database. They allow researchers to include the underlying reference sequence, as well as data tracks that annotate that sequence. Sequence is stored in the UCSC twoBit format, and the annotation tracks are stored in the same manner as Track Data Hubs. For more information on how to setup your own Assembly Data Hub, please refer to the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hub wiki</a> and see the <a href="hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a>.</p> <!-- ========== Viewing Hub Tracks in the Browser ==================== --> <a name="View"></a> -<h2>Viewing Track Hubs in the browser</h2> +<h2>Viewing Track Hubs</h2> +<h3>Public hubs</h3> <p> -<strong><em>Public hubs</em></strong><br> The Genome Browser provides links to a collection of public track hubs that have been registered -with UCSC. To view a list of the public track hubs available for the currently selected assembly, -click the "track hubs" button on the Genome Browser gateway or annotation tracks page. The -Public Hubs tab on the Track Hubs page lists the hubs that are available for display in the browser. -To add a hub to your display, click the "Connect" button next to the hub. You can also -click "Description" and "Hub Name" to see more details about some Public Hubs. -After connecting to the hub, click the "Genome Browser" link from the top blue bar. The -default assembly for the selected hub will be displayed with hub tracks in a separate track group -below the browser image. The tracks can be <a href="hgTracksHelp.html#FineTuning">configured and -manipulated</a> in the same fashion as native browser tracks. As with any very large track in the -Genome Browser, exercise caution when viewing a broad genomic region that requires the Genome -Browser to display a large number of track features: the browser display may time out.</p> -<p> -<strong><em>Unlisted hubs (located in the <a href="../../cgi-bin/hgHubConnect" target="_blank">My -Hubs</a> tab)</em></strong><br> -In addition to the publicly available hubs listed on the Public Hubs tab, it is possible to load -your own unlisted track hub or one created by a colleague as long as you know its URL. To add an -unlisted hub, open the Track Hubs page and click the <a href="../../cgi-bin/hgHubConnect" -target="_blank">My Hubs</a> tab. This tab lists the unlisted track hubs that you have loaded into -your browser. To import a new hub, type its URL into the text box, then click the Add Hub button. -If the track hub is imported successfully, it will be added to the list. It is also possible to add -a track hub by directly adding the hub's URL to the browser URL. If you add -<strong>hubUrl=[URL]</strong> to your hgTracks URL line, it will add the hub directly into the -browser (e.g., <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<strong>&hubUrl=</strong>http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt</a>). -If the hub you've selected is an assembly hub, the supported assemblies will be selectable from the -gateway page by selecting the name of the track hub in the group pulldown.</p> -<p> -If the browser is unable to load the track hub, it will display an error message. Some common causes -for an import to fail include typos in the URL, attempting to add a track hub from a different -assembly, a hub server that is offline, or errors in the track hub files. Once you have successfully -loaded a hub, you can view it in the browser by clicking the "Connect" button. Please note -that unlisted hubs are in no way secure. The URL helps to obfuscate the location of the data; it is -a simple barrier to casual users. Please also know that hubs can be loaded from a local directory -when using <a href="hubQuickStartAssembly.html#blatGbib" target="_blank">GBiB</a>.</p> -<p> -To remove a track hub from your Genome Browser display, click the "Disconnect" button on -the Track Data Hubs page.</p> -<p> -Occasionally, remote track hubs may be missing, off-line, or otherwise unavailable. If a user is -already browsing data from the remote hub when it disconnects, a yellow error message will be -displayed instead of the expected data.</p> -<p> -The track sets in hubs are genome assembly specific. The Track Hubs page lists each hub and the -assemblies it supports. To switch to a different assembly, click the Genomes link in the top menu -bar, then select the new assembly from the Gateway page. If the hub supports assemblies that are not -natively supported by UCSC or the mirror you're visiting, the assembly can be selected by choosing -the track hub name under the group menu.</p> +with UCSC. To view a list of the public track hubs available, click into the blue navigation bar +"My Data" and then "Track Hubs" to reach the +<a href="../../cgi-bin/hgHubConnect?#publicHubs">Public Track Hubs page</a>. +You can click links in the "Description" column to see details about a particular Hub. +To view a hub's data, click on an assembly name on the row of your +hub or the "Connect" button. If you clicked the "Connect" button, +choose your assembly or click the "Genome Browser" link from the top blue bar to be brought to the +default assembly. The selected hub tracks will be listed in a separate track group +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> 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>.</p> -<!--Question: Are there any restrictions to these uses?--> +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> +<h2>Sharing Track Hubs</h2> +<p>When sharing track hubs on a single assembly, we recommend using +<a href="../../cgi-bin/hgSession">Saved Sessions</a> +(especially for publications). These have the advantages +of being single-click access and sharing a full browser configuration. +If you are just starting, an overview of the process 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>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> +<p> +If you prefer URL manipulation, it is also possible to add or +<a href="../../FAQ/FAQlink.html#hubUrl" target="_blank">share a track hub directly by URL</a> +or otherwise <a href="../help/customTrack.html#optParams" +target="_blank">modify the browser via URL</a>. For example, 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 @@ -612,33 +629,33 @@ image.</p> <p> The track description file must have the same name as the symbolic name for the track (defined by the <em>track</em> tag in the trackDb.txt file) with a suffix of <em>.html</em>. For instance, a description file associated with the track named "dnaseSignal" in <em>Example 4</em> would be named "dnaseSignal.html". The description file must reside in the same directory as the trackDb.txt file.</p> <p> Both parent and child tracks within a super-track can have their own description files. If the description file is not present, the corresponding sections of the track settings and details pages are left blank. Only one description page can be associated with composite and multiWig tracks; the file name should correspond to the symbolic name of the top-level track in the composite.</p> <!-- ========== Debugging and Updating Track Hubs ============================== --> <a name="Debug"></a> -<h2>Debugging and updating Track Hubs</strong></h2> +<h2>Debugging Track Hubs</strong></h2> -<h3>Changing udcTimeout to debug hub display</h3> +<h3>Not updating? Change udcTimeout</h3> <p> As part of the track hub mechanism, UCSC caches data from the hub on the local server. The hub utility periodically checks the time stamps on the hub files, and downloads them again only if they have a time stamp newer than the UCSC one. For performance reasons, UCSC checks the time stamps every 300 seconds, which can result in a 5-minute delay between the time a hub file is updated and the change appears on the Genome Browser. Hub providers can work around this delay by inserting the CGI variable <em><strong>udcTimeout=1</strong></em> into the Genome Browser URL, which will reduce the delay to one second. To add this variable, open the Genome Browser tracks page and zoom or scroll the image to display a full browser URL in which the CGI variables visible. Insert the CGI variable just after the "hgTracks" portion of the URL so that it reads <em>http://genome.ucsc.edu/cgi-bin/hgTracks?<b>udcTimeout=1&</b></em> (with the remainder of the URL following the ampersand). To restore the default timeout, a warning message will appear on hgTracks with a link to clear the udcTimeout variable.</p> <a name="validate"></a> @@ -650,31 +667,31 @@ Hub Development tab</a>. After entering your URL in the search box, the tool runs the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">hubCheck utility</a> program equivalent to:</p> <pre>hubCheck -noTracks http://url.to.hub.txt</pre> <p> The noTracks setting speeds up the validation process but does not check for the presence or validity of your remotely hosted data track files. This tool checks your hub.txt, genome.txt, and trackDb.txt settings and displays warnings and errors in bright red font, such as "<font color="red">Missing required setting...</font>" and "<font color="red">Cannot open...</font>". The "Display load times" and "Enable hub refresh" optional settings show the load timing at the bottom of the Genome Browser page and allow instant hub refresh instead of 5 minute refresh. These options can be checked and activated by clicking "View Hub on Genome Browser". The following picture shows <a href="examples/hubExamples/hubGroupings/hub.txt">the example track grouping hub</a> with the warning that the hub has no hub description page, no configuration errors, -and "Dispay load times" checked:</p> +and "Display load times" checked:</p> <p class='text-center'> <img class='text-center' src="../../images/hubDevelopment.png" alt="The Hub Development tool checks config setting" width="749" height="249"> <p class='gbsCaption text-center'>The Hub Development tool checks for proper configuration files and track hub settings, and allows access to debugging settings.</p> </p> <h3>Check hub settings using hubCheck utility</h3> <p> It is a good practice to run the command-line utility <em>hubCheck</em> on your track hub when you first bring it online and whenever you make significant changes. This utility by default checks that the files in the hub are correctly formatted, but it can also be configured to check a few other things including that various trackDb settings are correctly spelled and that they are supported by the UCSC Genome Browser. You can read more about using hubCheck to check the @@ -689,123 +706,82 @@ -checkSettings - check trackDb settings to spec -version=[v?|url] - version to validate settings against (defaults to version in hub.txt, or current standard) -extra=[file|url] - accept settings in this file (or url) -level=base|required - reject settings below this support level -settings - just list settings with support level Will create this directory if not existing -noTracks - don't check remote files for tracks, just trackDb (faster) -udcDir=/dir/to/cache - place to put cache for remote bigBeds and bigWigs </code></pre> <p> Note that you will have to use the udcDir if /tmp/udcCache is not writable on your machine.</p> <p> The hubCheck program is available from the UCSC downloads server at <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">http://hgdownload.soe.ucsc.edu/admin/exe/</a>.</p> +<a name="troubleConnecting"></a> +<h3>Troubleshooting Track Hub connections</h3> +<p> +If the browser is unable to load a track hub, it will display an error message. Some common causes +for an import to fail include typos in the URL, a hub server that is offline, +or errors in the track hub configuration files. Occasionally, remote track +hubs may be missing, off-line, or otherwise unavailable. If a user is +already browsing data from the remote hub when it disconnects, a yellow error message will be +displayed instead of the expected data.</p> + <!-- ========== Setting Up Track Item Search ============================== --> <a name="Search"></a> <h2>Setting up track item search</h2> <p> The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support this behavior you have to add an index to the bigBed file when you initially create the the bigBed file from the bed file input. Indices are usually created on the name field of the bed, but can be created on any field of the bed. Free-text searches can also be enabled by creating a <a href="trix.html">TRIX index file</a> that maps id's in the track to free-text metadata. Further -intructions can be found in the <a href="hubQuickStartSearch.html">Searchable Hub Quick Start +instructions can be found in the <a href="hubQuickStartSearch.html">Searchable Hub Quick Start Guide</a>.</p> <p> See the searchIndex and searchTrix fields in the <a href="trackDb/trackDbHub.html">Hub Track Database Definition document</a> for information on how to set up your bigBed to enable searching. The searchIndex setting requires the input BED data to be case-senstive sorted (<code>sort -k1,1 -k2,2n</code>). You can use either the example UNIX <code>sort</code> command or the <code>bedSort</code> utility available <a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">here</a>. See an example <a href="examples/hubExamples/hubIndexedBigBedSearchable/" target="_blank">searchable hub</a>.</p> -<!-- ========== Displaying Track Hubs by URL and in Sessions ============================== --> -<a name="Session"></a> -<h2>Displaying Track Hubs by URL and in sessions</h2> -<p> -Once you have successfully loaded your hub, by pasting the URL to the location of your hub.txt file -into the <a href="../../cgi-bin/hgHubConnect" target="_blank">My Hubs</a> tab of the Track Data Hubs -page, you may want to consider building URLs to directly load the hub along with session -settings.</p> -<p> -To build a URL that will load the hub directly, add "<b>&hubUrl=</b>" to the hgTracks -CGI followed by the address of the hub.txt file. You also need to include the UCSC assembly you -are displaying the hub upon such as "db=hg19". For example, here is a working link that -will visualize the ENCODE AWG hub: -<pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?<b>db=hg19&hubUrl=</b>http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt </code></pre> -<p> -If you also want to load your hub at specific browser coordinates and with a specific set of other -browser tracks (you can also set the visibility of each track in your hub), you can save your -hub in a session, which are in essence "View Settings" collected in a text file (example -session text files <a href="../help/examples/sessions/" target="_blank">here</a>). Sessions can be -<a href="hgSessionHelp.html#HowToShare" target="_blank">shared</a> in different ways, -please see the instructions for <a href="hgSessionHelp.html#Create" target="_blank"> -creating a session and saving it to a file</a>.</p> -<p> -By making your session file available over the Internet, you can build a URL that will load the -session automatically by adding "<b>&hgS_loadUrlName=</b>" to the hgTracks CGI followed by -the URL location of the saved session file. The location of the saved session file should be in the -same directory that holds your hub.txt file. Finally add "<b>&hgS_doLoadUrl=submit</b>" -to the URL to inform the browser to load the session.</p> -<p> -There are four required variables for your URL to load a session with a hub and an example URL:</p> -<pre><code><strong>db</strong> - name of the assembly (e.g. hg19 or mm10) -<strong>hubUrl</strong> - URL to your track hub -<strong>hgS_loadUrlName</strong> - URL to your session file -<strong>hgS_doLoadUrl</strong> - value should be "submit" </code></pre> -<pre>http://genome.ucsc.edu/cgi-bin/hgTracks<strong>?db=</strong>hg19<strong>&hubUrl=</strong>http://myLab.org/myHub.txt<strong>&hgS_loadUrlName=</strong>http://mySession<strong>&hgS_doLoadUrl=submit</strong> </pre> -<p> -Another feature one can use in place of "<strong>&hubUrl=</strong>" is -"<strong>&hubClear=</strong>", 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, -ect.). This feature can be useful for dynamically generated hubs that might collect in the browser -otherwise.</p> - -<p> -Beyond the URL options of "<strong>&hubUrl=</strong>" and "<strong>&hubClear=</strong>" -there are many other <a href="../../FAQ/FAQlink.html" target="_blank">ways to link to the Browser</a> -including a list of <a href="../help/customTrack.html#optParams" -target="_blank">URL optional parameters</a> described in the the Custom Tracks User's Guide.</p> - <!-- ========== Registering a Track Hub with UCSC ==================== --> <a name="Register"></a> <h2>Registering a Track Hub with UCSC</h2> <p> If you would like to share your track hub with other Genome Browser users, you can register your hub with UCSC by contacting the Genome Browser technical support mailing list at <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. Please include the URL of your hub.txt file in the message. Once registered, your hub will appear as a link on the Public Hubs tab on the Track Hubs page. To assist developers of Public Hubs, there is a <a href="http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines">Public Hubs Guidelines</a> page. The page shares pointers and preferred style approaches, such as the need for creating description html pages for your data that display any available references and an email contact for further data questions.</p> <p> Alternatively, you can share your track hub with selected colleagues by providing them with the URL needed to load your hub via the My Hubs tab.</p> <!--Note: Probably should add a blurb about (lack of) security here. Maybe just expand this section to be about sharing hub data.--> <!-- ======== Testing hub compatibility between genome browsers ============== --> <a name="Compatibility"></a> -<h2>Testing hub compatibility between genome browsers</h2> +<h2>Checking Hub settings and Compatibility</h2> <p> Due to the growth in popularity of the track hub format, other genome browsers have begun supporting the UCSC track hub format. The hubCheck utility can be used to check the compatibility of your hub with the UCSC Genome Browser and other genome browsers. The following examples describe various settings that may be useful to you as you test this compatibility.</p> <p> <strong><em>Example 1:</em></strong> Listing the trackDb settings and their support levels and filtering them by support level.</p> <p> You can see all of the currently supported trackDb settings and their support level in the UCSC Genome Browser by running hubCheck with the "-settings" option:</p> <pre><code>$ hubCheck -settings </code></pre> @@ -1005,31 +981,31 @@ <img height="400px" src="../../images/cyverseSendToGenomeBrowser.png"> </div> <p>And then edit the fields of your <em>hub.txt</em>, <em>genomes.txt</em>, and <em>trackDb.txt</em> files like so:</p> <div class="text-center"> <img height="500px" width="1000px" src="../../images/cyverseEditedPaths.png"> </div> <p>To get the correct links to bigData files, again be sure to use the "Send To: Genome Browser" links in the menu. </p> <p> Please see the <a href="https://wiki.cyverse.org/wiki/display/DEmanual/Viewing+Genome+Files+in+a+Genome+Browser" target="_blank"> Viewing Genome Files in a Genome Browser</a> wiki page on the CyVerse wiki for more information (please note the difference of the Data Commons for final curated publication material, -and the Discovery Envirnoment for developing data). +and the Discovery Environment for developing data). Please direct any questions about CyVerse or the Discovery Environment to their <a href="http://www.cyverse.org/learning-center/ask-cyverse" target="_blank">Ask CyVerse</a> page or contact Cyverse support staff directly via the blue Intercom button on the bottom right of the Discovery Environment page. <!-- Galaxy stub <h3>Hosting Hubs on Galaxy</h3> <p> Galaxy is </p> --> <h3>Hosting Hubs on Github</h3> <p> <a href="https://github.com" target="_blank">Github</a> supports byte-range access to files when they are accessed via the <em><b>raw.githubusercontent.com</b></em> style URLs. To obtain a raw URL to a file already uploaded on Github, click on a file in your repository and click the <em>Raw</em> button:</p>