Controlling IGV through mozilla Firefox

Motivation

An add-on for Firefox Controlling IGV, the Integrative Genomics Viewer ( http://www.broadinstitute.org/igv/ ) , through mozilla Firefox .

Tested with Firefox 32.0.3 and IGV 2.2.4 .

Author

Pierre Lindenbaum PhD @yokofakun

Institut-du-thorax UMR1087, Nantes, France.

Installation

download the latest release: https://github.com/lindenb/igvfox/releases/latest

( or compile igvfox.xpi (see below ) and open-it from a firefox window )

Setting preferences

in menu 'Add-ons', select the IGVfox plugin and set the host:port of IGV

Example

The two files below must be downloaded:

There is an example under test/test01.html ( https://github.com/lindenb/igvfox/blob/master/test/test01.html )

The html page loads a small javascript code: ( https://github.com/lindenb/igvfox/blob/master/test/igvfox.js )

(...)
IGVFox._dipatchEvent = function(param)
	{
		var event = document.createEvent('CustomEvent');
       		event.initCustomEvent("igvfox@univ-nantes.fr", true, true, param );
       		document.documentElement.dispatchEvent(event); 
	};

IGVFox.goTo = function(position)
	{
	IGVFox._dipatchEvent(position);
	};
(...)

this code is called from a HTML page:

<tr>
  <td>rs2229482</td>
  <td>
    <a href="javascript:IGVFox.goTo('chr1:22071831-22071833')">chr1:22071832</a>
  </td>
</tr>

Open IGV, open test01.html in your browser , clicking on a hyperlink should invoke 'goto' in IGV.

Compilation

if needed, you can compile and package the firefox add-on igvfox.xpi using make

$ make igvfox.xpi