22a4ecd91a6aa015b9a8807b9c2c883c962ff694 dschmelt Wed Feb 19 14:48:27 2020 -0800 Documenting validate hub feature, edit2 #24429 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index ceed375..87567ee 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -636,42 +636,43 @@ 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> <h3>Check hub settings using Validate Hub tool</h3> <p> Hubs can be checked for valid file configuration, trackDb keywords, and composite or super track settings with the Validate Hub tool. This tool can be accessed from the Track Hub page under <a href="../../cgi-bin/hgHubConnect?#validateHub">the Validate Hub tab</a>. After entering your URL in the search box, -the tool runs hubCheck with the following settings:</p> +the tool runs hubCheck like so:</p> <pre>hubCheck -noTracks http://url.to.hub.txt</pre> <p> -Note that for speed, the noTracks setting was added and the Validate Hub tool does not check -presence of your remotely hosted data track files. This tool checks your hub.txt, genome.txt, -and trackDb.txt settings. The following picture shows +The noTracks setting speeds up the validation process but does not check for +the presence of your remotely hosted data track files. This tool checks your hub.txt, +genome.txt, and trackDb.txt settings and displays errors in bright red font, such +as "<font color="red">Missing required setting...</font>" and "<font color="red">Cannot open...</font>". The following picture shows <a href="examples/hubExamples/hubGroupings/hub.txt">the example track grouping hub</a> -showing no configuration errors:</p> +with no configuration errors:</p> <p class='text-center'> <img class='text-center' src="../../images/validateHub.png" alt="Validate hub tool checks config setting" width="749" height="249"> - <p class='gbsCaption text-center'>The validate hub tool checks for valid hub settings.</p> + <p class='gbsCaption text-center'>The validate hub tool checks for proper configuration files and track hub 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 compatibility of your hub with other genome browsers <a href="#Compatibility"</a>below</a>. <p> Here is the usage statement for the hubCheck utility: <pre><code>hubCheck - Check a track data hub for integrity. usage: