d60963c11b6d1f67e678c6ff2cf9c82f2ada9e12 lrnassar Tue Mar 26 17:28:58 2024 -0700 Encouraging session use as the first option when sharing custom tracks, refs #23842 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index e2f25fc..8b15c48 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -729,32 +729,43 @@ <a href="../help/hgBamTrackHelp" target="_blank">configuring BAM tracks</a> and the <a href="../help/hgWiggleTrackHelp.html" target="_blank">configuring graph-based tracks</a> help pages to learn how to further change the display.</li> </ul> <a name="SHARE"></a> <h2>Sharing your annotation track with others</h2> <p> To make your Genome Browser annotation track viewable by people on other machines or at other sites, follow the steps below.</p> <p> <strong>Step 1. Put your formatted annotation file on your web site.</strong> <p> Be sure that the file permissions allow it to be read by others.</p> <p> -<strong>Step 2. Construct a URL that will link this annotation file to the Genome Browser.</strong> +<strong>Step 2. Create a session link, or construct a URL that will link this annotation file to the Genome Browser.</strong> <p> +The easiest way to share custom tracks is through the use of +<a href=../help/hgSessionHelp.html>sessions</a>. First, upload your tracks as +discussed in the <a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a> section. +Then create a named session that includes your custom tracks by navigating to the "Sessions" +page through the "My Data" section in the menu bar. Once there, follow the instructions in the +<a href=../help/hgSessionHelp.html#Create>Creating a Session</a> section of the Sessions help page. +Once you have saved your custom track into a named session, you can share that session with others +by sharing the URL from the "Browser" link or emailing it to them directly by clicking +the "Email" link.</p> +<p> +Alternatively, you can create a URL. The URL must contain 3 pieces of information specific to your annotation data:</p> <ul> <li> The species or genome assembly on which your annotation data is based. To automatically display the most recent assembly for a given organism, set the <em>org</em> parameter: <em>e.g.</em> <code>org=human</code>. To specify a particular genome assembly for an organism, use the <em>db</em> parameter, <code>db=<databaseName></code>, where <em>databaseName</em> is the UCSC code for the genome assembly. For a list of these codes, see the Genome Browser <a href="/FAQ/FAQreleases.html#release1" target="_blank">FAQ</a>. Examples of this include: db=hg38 (Human Dec. 2013 assembly = GRCh38), db=mm10 (Mouse Dec. 2011 assembly = GRCm38).</li> <li>Additionally, particular genome assemblies, including assemblies in assembly hubs, can be specified using the <em>genome</em> parameter, <code>genome=<databaseName></code>, which acts in the same manner as the <em>db</em> parameter. Here is an example using the house mouse (<i>Mus musculus</i>, 129S1_SvImJ) assembly hub: <a href="http://genome.ucsc.edu/cgi-bin/hgTracks?genome=129S1_SvImJ&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt" @@ -767,40 +778,34 @@ <li> The URL of the annotation file on your web site. This information is of the form <code>hgt.customText=<url></code> or <code>hgct_customText=<url></code>, where <em>url</em> points to the annotation file on your website. An example of an annotation file URL is <a href="test.bed" target="_blank">http://genome.ucsc.edu/goldenPath/help/test.bed</a>.</li> </ul> <p> Combine the above pieces of information into a URL of the following format (the information specific to your annotation file is highlighted):</p> <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em><organismName></em></font>&position=<font color="000099"><em><chrPosition></em></font>&hgt.customText=<font color="000099"><em><url></em></font></code></pre> <p> <strong>Step 3. Provide the URL to others.</strong></p> <p> -To upload a custom annotation track from a URL into the Genome Browser, paste the URL into the large -text edit box on the Add Custom Tracks page, then click the Submit button.</p> +If you created a <a href=../help/hgSessionHelp.html>session</a>, that stable link can be freely shared.</p> <p> -Custom Tracks can also be shared with others through named sessions. First, upload your tracks as -discussed in the <a href="#ADD_CT">Loading a Custom Track into the Genome Browser</a> section. Then create a named session that includes your custom tracks by navigating to the "Sessions" -page through the "My Data" section in the menu bar. Once there, follow the instructions in the -<a href=../help/hgSessionHelp.html#Create>Creating a Session</a> section of the Sessions help page. -Once you have saved your custom track into a named session, you can share that session with others -by sharing the URL from the "Browser" link or emailing it to them directly by clicking -the "Email" link.</p> +Otherwise, to upload a custom annotation track from a URL into the Genome Browser, paste the URL into the large +text edit box on the Add Custom Tracks page, then click the Submit button.</p> <p> For integration into your own website e.g. in an html IFRAME, you can obtain the track image only, without the rest of the genome browser user interface, by replacing hgTracks in the URL with hgRenderTracks, such as in this example:</p> <pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630" target="_blank">http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630</a></code></pre> <p> If you'd like to share your annotation track with a broader audience, send the URL for your track—along with a description of the format, methods, and data used—to the UCSC Genome mailing list <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. <!-- above address is genome at soe.ucsc.edu --> <a name="OPTIONAL"></a> <h3>Optional URL parameters</h3>