From: Andreas Tille <tille@debian.org>
Subject: The original way to open Help text ends up in an exception
 Setting the explicit file name as well as avoiding the call to
   ClassLoader.getSystemResource
 helps fixing this.  Specifically the later is important, see
   https://lists.debian.org/debian-med/2012/11/msg00073.html

--- a/uk/ac/babraham/FastQC/FastQCMenuBar.java
+++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java
@@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu
 		}
 		else if (command.equals("help_contents")) {
 			try {
-				new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
+				new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
 			} 
 			catch (UnsupportedEncodingException e1) {
 				e1.printStackTrace();