Problem with using IGV

Question

[Chenglin]

Hi all,

I download IGV onto the server I am using and unzip it. In the folder which IGV_2.3.40.zip was unzipped, I typed the command java -Xmx750m -jar igv.jar to try if it works or not as guided in the readme.txt file. and the error showed below. I don't know what's wrong. Any help is very welcome!

Thanks!

Chenglin

INFO [2014-11-18 21:52:07,836]  [DirectoryManager.java:149] [main]  IGV Directory: /home/chenglin/igv
INFO [2014-11-18 21:52:07,836] [DirectoryManager.java:149]  IGV Directory: /home/chenglin/igv
INFO [2014-11-18 21:52:07,841]  [Main.java:85] [main]  Startup  IGV Version 2.3.40 (48)11/03/2014 01:03 PM
INFO [2014-11-18 21:52:07,841]  [Main.java:86] [main]  Java 1.8.0_20
INFO [2014-11-18 21:52:07,841]  [DirectoryManager.java:58] [main]  Fetching user directory... 
INFO [2014-11-18 21:52:07,942]  [Main.java:87] [main]  Default User Directory: /home/chenglin
INFO [2014-11-18 21:52:07,942]  [Main.java:88] [main]  OS: Linux
GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://projects.gnome.org/gconf/ for information. (Details -  1: Not running within active session)
GConf Error: Failed to contact configuration server; some possible causes are that you need to enable TCP/IP networking for ORBit, or you have stale NFS locks due to a system crash. See http://projects.gnome.org/gconf/ for information. (Details -  1: Not running within active session)
ERROR [2014-11-18 21:52:08,482]  [DefaultExceptionHandler.java:42] [main]  Unhandled exception
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
    at java.awt.Window.<init>(Window.java:536)
    at java.awt.Frame.<init>(Frame.java:420)
    at java.awt.Frame.<init>(Frame.java:385)
    at javax.swing.JFrame.<init>(JFrame.java:181)
    at org.broad.igv.ui.Main.main(Main.java:67)

Answer 1

[GouthamAtla]

use -X while logging in to server and start IGV. e.g.:

ssh username@server -X

[Chenglin]

What is the option -X for? Can you explain a bit more? I could log in, I just could not run the software. Thanks!

[GouthamAtla]

It's X11 forwarding, to run GUI programs from a remote machines via ssh.

[Chenglin]

Got it. Thanks! Is it safe to use this method?