f1900dde9063ea0a4887c3f2d96fd8c29c9a1d6a jnavarr5 Tue Feb 24 15:49:58 2026 -0800 Adding information about Hub Space to the NAR help documentation. Changing relative links to CGIs to absolute when possible. Adding a missing <p> tag on the track hub help page, and adding information about hub space, refs #36893 diff --git src/hg/htdocs/goldenPath/help/hgSessionHelp.html src/hg/htdocs/goldenPath/help/hgSessionHelp.html index 41cbfe8f635..a31c530e812 100755 --- src/hg/htdocs/goldenPath/help/hgSessionHelp.html +++ src/hg/htdocs/goldenPath/help/hgSessionHelp.html @@ -541,40 +541,50 @@ <a name="NAR"></a> <h2>Help for Nucleic Acids Research submitters</h2> <p> The Nucleic Acids Research (NAR) journal now <a href = "https://academic.oup.com/nar//pages/data_deposition_and_standardization" target = _blank>requires</a> manuscript submissions to contain a private Session link to your data in the UCSC Genome Browser that allows reviewers to access data. These instructions will show you how to upload, view, and share your data.</p> <!-- ====Uploading custom data=================== --> <a name="custom_data"></a> <h3>Viewing your data on the Genome Browser</h3> <p> You can view your own private data by uploading your annotation files to the Genome Browser as <em>custom tracks</em>; visit our <a href="customTrack.html">custom track help page</a> to learn -more. To summarize the steps to upload your data, you will need to:</p> +more. For binary-indexed files, such as bigBed, bigWig, BAM, and VCF, you will need to host the file +on a web-accessible server. Please view the <a href="/goldenPath/help/hgTrackHubHelp.html#Hosting" +target="_blank">Hosting</a> section of the Track Hub Help documentation for available resources. +</p> + +<p> +To summarize the steps to upload your data, you will need to:</p> <ol> <li> Ensure the data file is <a href="customTrack.html#format">formatted correctly.</a></li> + <li> + Upload the data file to a web-accessbile server provided by your own institution or another + external resource, such as <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect?#hubUpload" + target="_blank">Hub Space</a>, if necessary.</li> <li> Create a <a href="customTrack.html#TRACK">track line</a> for your custom track.</li> <li> <a href="customTrack.html#ADD_CT">Load the custom track</a> by adding your track line to our - <a href="../../cgi-bin/hgCustom">Custom Tracks</a> page.</li> + <a href="/cgi-bin/hgCustom">Custom Tracks</a> page.</li> <li> View the data in the Genome Browser.</li> </ol> <!-- ====Custom track examples=================== --> <a name="custom_examples"></a> <h3>Custom track examples</h3> <p> Creating the track line may be the most challenging step since many configuration options exist. The track line begins with the <strong>track</strong> keyword, followed by one or more <a href="customTrack.html#TRACK">attribute=value</a> pairs where the order of the attributes does not matter. Here are some examples:</p> <h6>BAM custom track</h6> <p> The simplest example of a BAM custom track is the following track line: @@ -601,139 +611,141 @@ <strong>description</strong> atrributes: <pre><code>track type=bam visibility=dense name="My BAM" description="Example from the ENCODE RNA-seq CSHL track" bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLongRnaSeqA549CellPapAlnRep1.bam</code></pre></p> <p> There are also options to <a href="hgBamTrackHelp.html">configure the display</a> of your BAM files, such as a <em>density plot feature</em> that will dynamically process the underlying BAM into a wiggle signal.</p> <hr> <h6>bigWig custom track</h6> <p> A bigWig file is useful when trying to display dense, continuous data. Read more on the <a href="bigWig.html">bigWig track format</a> help page. Here is an example bigWig track that is colored red, instead of the default black color, that can be pasted directly into the -<a href="../../cgi-bin/hgCustom">Custom Tracks Page</a>: +<a href="/cgi-bin/hgCustom">Custom Tracks Page</a>: <pre><code>track color=255,0,0 name="HeLa-S3 nucleus minus signal" description="RNA Subcellular CAGE Localization from ENCODE/RIKEN" type=bigWig visibility=full bigDataUrl=http://hgdownload.gi.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeRikenCage/wgEncodeRikenCageHelas3NucleusPapMinusSignalRep1.bigWig</code></pre></p> <p> There are also options to <a href="hgWiggleTrackHelp.html">configure the display</a> of your wiggle tracks, such as changing the track height or type of graph.</p> <!-- ====Creating a session====================== --> <a name="NAR_session"></a> <h3>Creating a session for NAR publications</h3> <p> After creating your custom tracks and viewing your data on the Genome Browser, you can save all of your tracks and settings to a snapshot of the Genome Browser called a <em>session</em>. You can easily save a session by following these five steps:</p> <ol> <li> <strong>Configure the Genome Browser to your preference</strong><br> Make sure the display of your custom tracks is to your liking on the Genome Browser.</li> <li> <strong>Navigate to the sessions page</strong><br> Once you are satisfied with the display, go to the - <a href="../../cgi-bin/hgSession">My Sessions</a> page by either: + <a href="/cgi-bin/hgSession">My Sessions</a> page by either: <ul> <li> Going to <em><strong>My Data</strong></em> -> <em><strong>My Sessions</strong></em> from the navigation bar.</li> <li> Using the "<em><strong>s</strong> then <strong>s</strong></em>" keyboard shortcut - when viewing the main page of the <a href="../../cgi-bin/hgTracks">Genome Browser</a>.</li> + when viewing the main page of the <a href="/cgi-bin/hgTracks">Genome Browser</a>.</li> </ul></li> <li> <strong>Login to the UCSC Genome Browser</strong><br> You must sign in to be able to save named sessions which will then be displayed with Browser and Email links.</li> <li> <strong>Save your session</strong><br> Go to the <strong>Save Settings</strong> section and in the <em>Save current settings as named session</em> text box, and enter a name for your session. When saving the session, be sure to have the "<em>allow this session to be loaded by others</em>" option checked and then click <em><strong>submit</strong></em>. <ul> <li>You should then be able to copy and share a link similar to the following: <code>http://genome.ucsc.edu/s/YourUserName/YourSessionName</code></p></li> </ul> <li> <strong>Edit the session description</strong><br> Once the session is created, under the "view/edit details" column you can click the <em><strong>view/edit</strong></em> button to add a description to the session.</li> <hr> <li> <strong>Publish your session as a Public Session for public discovery</strong><br> If you eventually make a Public Session of your session after your paper is published, and provide a detailed description, anyone can find it by searching for terms you share. <ul> - <li>For example, navigate to the <a href="../../cgi-bin/hgPublicSessions">Public Sessions</a> + <li>For example, navigate to the <a href="/cgi-bin/hgPublicSessions">Public Sessions</a> page and search "NAR" to see some example sessions. Or click this link, which adds <a href="../../cgi-bin/hgPublicSessions?search=NAR" target="_blank"><code>?search=NAR</code></a> to the URL.</li> <li>As a Public Session, your session can then be found by anyone entering a search term, where you can even create a <a href="sessions.html#lab" target="_blank">gallery of Public Sessions</a> related to your search by using a unique string in your descriptions.</li> <li>Here is an example "gallery" of all sessions that have the word "sessionView" in their descriptions: <a href="http://genome.ucsc.edu/cgi-bin/hgPublicSessions?search=sessionView" target="_blank">http://genome.ucsc.edu/cgi-bin/hgPublicSessions?search=sessionView</a></li> </ul> </ol> <!-- ====Sharing the session===================== --> <a name="NAR_sharing"></a> <h3>Sharing your session link</h3> <p> After saving your session, you will now be able to share your session link with others. There are three different ways that you can share your session: </p> <ol> <li> Immediately after creating a new session, the top of the page offers a <em>Browser</em> hyperlink that will allow you to view the newly saved session. You can right-click the <em><strong>Browser</strong></em> link to save the URL.</li> <li> Alternatively, you can right-click the session name and then click <em>Copy Link Address</em> to save the session URL.</li> <li> - Adding your session to the <a href="../../cgi-bin/hgPublicSessions">Public Sessions</a> page + Adding your session to the <a href="/cgi-bin/hgPublicSessions">Public Sessions</a> page will provide a useful way of sharing your session with the world in the long run. You can add your session to our Public Sessions by selecting the "<em>post in public listing?</em>" checkbox.</li> </ol> <h6>Editing the session URL</h6> <p> You can edit URLs to directly go to different parts of the Genome Browser such as by changing <strong>hgSession</strong> to <strong>hgTracks</strong>, e.g., <pre><code>http://genome.ucsc.edu/cgi-bin/<strong>hgTracks</strong>?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.rela</code></pre></p> <p> Having <strong>hgTracks</strong> in the session URL will take the viewer to the main page of the Genome Browser instead of the sessions page.</p> <!-- ====Creating a hub========================== --> <a name="NAR_hub"></a> <h3>Using track hubs to organize custom tracks</h3> <p> Creating a track hub allows you to group and organize your annotation tracks, but is limited to <a href="hgTrackHubHelp.html#Setup">compressed binary indexed formats</a> that can be remotely hosted. This will require the use of a web-accessible location to load the track hub in the UCSC Genome Browser. If your institution does not provide web space for you, you can look into hosting your binary files at a couple different web hosting services, such as -<a href="http://www.cyverse.org/">CyVerse</a> or <a href="https://figshare.com/">figshare</a>. If +<a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect?#hubUpload" target="_blank">Hub Space</a>, +<a href="http://www.cyverse.org/" target="_blank">CyVerse</a>, or +<a href="https://figshare.com/" target="_blank">figshare</a>. If you would like to learn more about using track hubs, please read our <a href="hgTrackHubHelp.html">Track Hub help page</a>.</p> <!-- ====Genome Browser inquiries================ --> <h3>Genome Browser inquiries</h3> <p> If you have any questions regarding the creation of your custom track or session, please feel free to <a href="../../contacts.html">contact us</a>. Before submitting a question, we strongly encourage you to search our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a>, our <a href="../../FAQ">website</a>, and our <a href="http://genomewiki.gi.ucsc.edu/index.php/Main_Page">wiki</a> for the answer. <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->