View source for Embedding CoGe JBrowse in your website

__NOTOC__
There are two ways to create a web page containing a CoGe JBrowse instance. 
# Embed the instance in an [https://developer.mozilla.org/en-US/docs/Web/HTML/Element/iframe IFRAME]
# Host the files on your server and only connect to CoGe's JBrowse API to get the actual track data.

==First Way: iframe==
start with the following HTML code:
<pre>
 <html>
  <body>
   <iframe src="https://genomevolution.org/coge/GenomeView.pl?gid=16911&embed=1" style="width:100%;height:100%"></iframe>
  </body>
 </html>
</pre>

JBrowse is put inside an IFRAME. The embed=1 parameter in the src URL tells CoGe to not display its normal page header and footer. Use whatever method you prefer (i.e. hard code or programmatically with javascript) to set the “gid” parameter. It is the CoGe genome id for the genome you wish to browse. Change the width and height styles if you have other HTML on your page and want the IFRAME to occupy less than the whole page.

Note that genome id for a genome can be found on the GenomeInfo page for the genome (https://genomevolution.org/coge/GenomeInfo.pl?gid=16911). Or by using CoGe’s API, https://genomevolution.org/wiki/index.php/Web_Services_RESTful_API

==Second Way: Hosting JBrowse files, pulling data from CoGe==
If you want to host most of the files on your own server:
download the web/js/jbrowse directory from github (https://github.com/LyonsLab/coge)
put the files on your server to match the hrefs below (js/jbrowse…) or change the hrefs
pass in the gid= parameter in the URL to your page, or modify the “var gid =..” line below
<pre>
<html>
<head>
<link rel="stylesheet" type="text/css" href="js/jbrowse/genome.css" />
<script type="text/javascript" src="js/jbrowse/src/dojo/dojo.js" data-dojo-config="async: 1"></script>
<script type="text/javascript" src="js/jbrowse/src/JBrowse/init.js"></script>
<script type="text/javascript">
    window.onerror=function(msg){
        if( document.body )
            document.body.setAttribute("JSError",msg);
    }

    var JBrowse;
    function init_JBrowse(id, callback) {
	    require( { baseUrl: 'js/jbrowse/src',
	    		   packages: [ 'dojo', 'dijit', 'dojox', 'jszlib',
	    		               { name: 'lazyload', main: 'lazyload' },
	    		               'dgrid', 'xstyle', 'put-selector',
	    		               { name: 'jDataView', location: 'jDataView/src', main: 'jdataview' },
	    		               'JBrowse'
	    		             ]
	      		 },
	      	['JBrowse/Browser', 'dojo/io-query', 'dojo/json' ],
	        function (Browser,ioQuery,JSON) {
	      		var queryParams = ioQuery.queryToObject( window.location.search.slice(1) );
	            var gid = queryParams.gid || queryParams.dsgid || 22736;
	            //var dataRoot = queryParams.data || 'data';
	            var config = {
	                containerID: id,
	                browserRoot: 'js/jbrowse/',
	                refSeqs: 'https://genomevolution.org/services/JBrowse/service.pl/config/refseq/?gid='+gid,//refSeqs: dataRoot + "/seq/refSeqs.json",
	                baseUrl: '/',//'jbrowse/',//dataRoot+'/', // mdb changed 1/15/14 for JBrowse-1.11.1
	                include: ['https://genomevolution.org/services/JBrowse/service.pl/config/tracks/?gid='+gid],//include: ['jbrowse_conf.json', dataRoot + "/trackList.json"],
	                //nameUrl: dataRoot + "/names/root.json",
	                defaultTracks: "sequence",//"sequence,features"
	                queryParams: queryParams,
	                location: queryParams.loc || '1:1..150000',//queryParams.loc,
	                forceTracks: queryParams.tracks,
	                initialHighlight: queryParams.highlight,
	                datasets: null,
	                show_nav: 1,//queryParams.nav,
	                show_tracklist: 1,//queryParams.tracklist,
	                show_overview: 1,//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: false
	            };

	            JBrowse = new Browser( config );
	            if (callback) callback(JBrowse);
	      	}
	    );
    }
</script>
</head>
<body>
<div id="jb" style="height:100%;width:100%;padding:0;">loading...</div>
<script>
    init_JBrowse('jb');
</script>
</body>
</html>
</pre>

==Examples==
* Embedded CoGe Genome Browser in the CyVerse wiki: https://pods.iplantcollaborative.org/wiki/display/sciplant/Test+of+CoGe+Genome+Browser+in+iFrame