87eae20de868054a5abeedeb78a24d3e296b87d5 dschmelt Tue May 21 15:09:55 2019 -0700 Adding notes about TinyURL enabling URL parameters #23030 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index d1f14dd..52f72b4 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -19,46 +19,55 @@ <li><a href="#hgsid">The hgsid parameter</a></li> <li><a href="#moreInfo">Additional URL parameters</a></li> </ul> <a name="link1"></a> <h2>Creating a sharable URL to view specific tracks</h2> <h6>How do I create a link to the Genome Browser to share my data?</h6> <p> The easiest way to save and share tracks from the URL is by <a href="../cgi-bin/hgLogin" TARGET="_blank">logging in</a> to your Genome Browser account and creating a <a href="../goldenPath/help/hgSessionHelp.html">saved session</a>. Saved sessions are a versatile way to share data that may include native annotations, Custom Tracks, Track Hubs, and Assembly Hubs. Note that the <input> format indicates a user choice and not a valid example.</p> <p> -You will be able to share Genome Browser sessions with the following link format: +You will be able to share Genome Browser sessions with the following link format:</p> <p><code>http://genome.ucsc.edu/s/<userName>/<sessionName></code></p> <p> For instructions on creating a saved session, go to the <a href="../goldenPath/help/hgSessionHelp.html#Create" target ="_blank">session user guide</a>. If you want to specify track settings in a URL directly, please read the section on -<a href="#trackViz">setting track visibility via URL</a> for a complete description. -Note that URL parameters do not work with the shorter session URLs. </p> +<a href="#trackViz">setting track visibility via URL</a> for a complete description. </p> <p> -Or if you prefer a modifiable, longer URL, use the following format:</p> -<p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<SessionName></code></p> -<p>It has the advantage of being able to add additional URL parameters to the end and the -flexibility of replacing "hgTracks" with different tools to share saved settings on the Table -Browser (hgTables), Variant Annotation Integrator (hgVai), or Data Integrator (hgIntegrator). -This will preserve your option selections and can be useful to share.</p> +Or if you prefer the older style, which allows you to link to different tools, you may use the +following format:</p> +<p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&gS_otherUserSessionName=<SessionName></code></p> +<p> +This longer format has the flexibility of replacing "hgTracks" with different tool names to share +saved settings on the Table Browser (hgTables), Variant Annotation Integrator (hgVai), or Data +Integrator (hgIntegrator). This will preserve your option selections and can be useful to share. +The following format will bring the recipient to a user's custom Table Browser selections:</p> +<p><code>http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=<userName>&hgS_otherUserSessionName=<SessionName></code></p> + +<p>Both session link formats have the advantage of being able to add URL parameters to the end. +The shorter link format requires a question mark before any URL parameters, with ampersand +characters separating different parameters like so: </p> +<p><code><a href=http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18>http://genome.ucsc.edu/s/view/clinicalzoom?textSize=18</a></code></p> +<p>The longer format requires an ampersand between each parameter, like so:</p> +<p><code><a href=http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&textSize=18>http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=view&hgS_otherUserSessionName=clinicalzoom&textSize=18</a></code></p> <a name="link2"></a> <h2>Linking to the Browser at a specific position</h2> <h6>How do I make a link to a specific genome or position?</h6> <p> You can link to a specific genome assembly and position in the Genome Browser using a URL with the <code>db=</code> and <code>position=</code> parameters. Note that the <input> format indicates a user choice and not a valid example.</p> <p><code>http://genome.ucsc.edu/cgi-bin/hgTracks?db=<assembly>&position=<position></code></p> <p> Where:</p> <ul> <li> <code>db</code> - designates a specific genome assembly. For example, <code>db=hg19</code> refers to the Feb. 2009 human genome release. For a list of db parameter values that @@ -72,32 +81,32 @@ <p><code><a href="../cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:35000-40000</a></code></p> <a name="trackViz"></a> <h2>Setting Track Visibility via URL</h2> <h6>How do I create a custom URL to control the visibility of specific tracks?</h6> <p> You can control the visibility of tracks from the URL with the following parameters, each linked by the "&" sign, similar to position parameters. For more information, please see the <a href="../goldenPath/help/customTrack.html#optParams" target ="_blank">optional URL parameters</a> section of the Custom Tracks User's Guide. Note that the <input> format indicates a user choice and not a valid example.</p> <ul> <li><code>hideTracks=1</code> - hides all tracks</li> <li><code><trackName>=hide|dense|pack|full</code> - sets specified track or subtrack to a chosen visibility</li> -<li><code>textSize=<number></code> - sets browser text size to a chosen number, default of -8 and maximum of 24</li> +<li><code>textSize=<number></code> - sets browser text size to either 6,8,10,12,14,18,24,or +34. Default is a textSize of 8.</li> <li><code>ignoreCookie=1</code> - removes pre-existing user settings like track seletion, custom tracks, and track hubs</li> </ul> <p> For example, you can use the following command to hide every track (hideTracks=1) and set the knownGene track to the pack visibility (knownGene=pack):</p> <p><code><a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene=pack</a></code></p> <p>Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.</p> <ul> <li><code><trackName>_hideKids=1</code> - hides a specific composite track's subtracks</li> <li><code><trackName>_sel=1</code> - selects specific subtrack to be 'checked', allowing display</li> </ul>