tripal_jbrowse/theme/node--jbrowse-instance.tpl.php

<script type="text/javascript" src="/jbrowse/Lentil/src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: '/jbrowse/Lentil/src'"></script>
<script type="text/javascript" src="/jbrowse/Lentil/src/JBrowse/init.js"></script>

<script type="text/javascript">
    window.onerror=function(msg){
        if( document.body )
            document.body.setAttribute("JSError",msg);
    }

    // add this.resolveUrl() on 1537-1538 of src/JBrowse/Browser.js
    // add /jbrowse/Lentil on 69 of src/dojo/dojo.js

    // puts the main Browser object in this for convenience.  feel
    // free to move it into function scope if you want to keep it
    // out of the global namespace
    var JBrowse;
    require(['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
         function (Browser,ioQuery,JSON) {
               // the initial configuration of this JBrowse
               // instance

               // NOTE: this initial config is the same as any
               // other JBrowse config in any other file.  this
               // one just sets defaults from URL query params.
               // If you are embedding JBrowse in some other app,
               // you might as well just set this initial config
               // to something like { include: '../my/dynamic/conf.json' },
               // or you could put the entire
               // dynamically-generated JBrowse config here.

               // parse the query vars in the page URL
               var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );

               var config = {
                   containerID: "JBrowseInstance",

                   dataRoot: '/jbrowse/Lentil/data',
                   browserRoot: '/jbrowse/Lentil',
                   queryParams: queryParams,
                   location: queryParams.loc,
                   forceTracks: queryParams.tracks,
                   initialHighlight: queryParams.highlight,
                   show_nav: queryParams.nav,
                   show_tracklist: queryParams.tracklist,
                   show_overview: queryParams.overview,
                   stores: { url: { type: "JBrowse/Store/SeqFeature/FromConfig", features: [] } },
                   makeFullViewURL: function( browser ) {

                       // the URL for the 'Full view' link
                       // in embedded mode should be the current
                       // view URL, except with 'nav', 'tracklist',
                       // and 'overview' parameters forced to 1.

                       return browser.makeCurrentViewURL({ nav: 1, tracklist: 1, overview: 1 });
                   },
                   updateBrowserURL: true
               };

               //if there is ?addFeatures in the query params,
               //define a store for data from the URL
               if( queryParams.addFeatures ) {
                   config.stores.url.features = JSON.parse( queryParams.addFeatures );
               }

               // if there is ?addTracks in the query params, add
               // those track configurations to our initial
               // configuration
               if( queryParams.addTracks ) {
                   config.tracks = JSON.parse( queryParams.addTracks );
               }

               // if there is ?addStores in the query params, add
               // those store configurations to our initial
               // configuration
               if( queryParams.addStores ) {
                   config.stores = JSON.parse( queryParams.addStores );
               }

               // create a JBrowse global variable holding the JBrowse instance
               JBrowse = new Browser( config );
    });

</script>

<div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
  <div class="content clearfix"<?php print $content_attributes; ?>>
    <div id="JBrowse" style="height: 700px;">
      <div id="JBrowseInstance" ></div>
    </div>
  </div>
</div>