bbe7c3ee9e306ef4cf003321c8c420f1c68f5d3e jnavarr5 Tue May 14 14:11:38 2024 -0700 Reformatting the 'creating a session' steps, refs #19736 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index e53398c..d0fcb25 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -736,41 +736,53 @@ <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 in a web-accessible location</strong> <p> Be sure that the file permissions allow it to be read by others.</p> <p> <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. +<a href=../help/hgSessionHelp.html>sessions</a>. 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> +the "Email" link. You can create a session with the following steps:</p> +<ol> + <li> + Upload your tracks as discussed in the <a href="#ADD_CT">Loading a custom track into the + Genome Browser</a> section.</li> + <li> + Configure the Genome Browser to appear as you wish. These settings will always be restored when + the Session URL is accessed.</li> + <li> + Navigate to the "Sessions" page through the "My Data" section in the menu + bar.</li> + <li> + Create a named session that includes your custom tracks. Detailed instructions for creating a + named session can be found on the <a href=../help/hgSessionHelp.html#Create>Creating a + session</a> section of the Sessions help page.</li> +</ol> <p> -Alternatively, you can create a URL. -The URL must contain <b>3 pieces of information</b> specific to your annotation data:</p> +Alternatively, you can create a URL using parameters to specify the assembly, genome position, and +custom track data. The URL must contain <b>3 pieces of information</b> specific to your annotation +data:</p> <ol> <li> The <b>species or genome assembly</b> 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> <ul> <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"