X11 error when running IGV from command line

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paul

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Nov 3, 2016, 9:59:48 AM11/3/16
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Hello,

When I executed IGV.sh with a batch script on a MacOS 10.10 inside of a PuTTY session, I get following error:

INFO [2016-11-03 09:54:42,099]  [DirectoryManager.java:149] [main]  IGV Directory: /Volumes/DataBackup/Share/refs/igv
INFO [2016-11-03 09:54:42,107]  [Main.java:82] [main]  Startup  IGV Version 2.3.26 (30)01/21/2014 10:36 AM
INFO [2016-11-03 09:54:42,126]  [Main.java:83] [main]  Java 1.7.0_76
Fetching user directory... INFO [2016-11-03 09:54:42,224]  [Main.java:84] [main]  Default User Directory: /Users/asdf
INFO [2016-11-03 09:54:42,225]  [Main.java:85] [main]  OS: Mac OS X
ERROR [2016-11-03 09:54:42,325]  [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:535)
        at java.awt.Frame.<init>(Frame.java:420)
        at java.awt.Frame.<init>(Frame.java:385)
        at javax.swing.JFrame.<init>(JFrame.java:180)
        at org.broad.igv.ui.Main.main(Main.java:64)



How do I fix this? Thank you,

Paul

James Robinson

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Nov 3, 2016, 11:21:51 AM11/3/16
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Have you set your X11 display variable?  Does the program "xclock" work for you?

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paul

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Nov 4, 2016, 10:47:38 AM11/4/16
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Hi Jim,

I know nothing about X11. 'xclock' does not exist on MacOSX.

Is there anyway to run igv with a batch script without it opening an application window? I'm trying to automate the process of generating coverage graps from a BAM file.

Thank you,
Paul



On Thursday, November 3, 2016 at 11:21:51 AM UTC-4, Jim Robinson wrote:
Have you set your X11 display variable?  Does the program "xclock" work for you?
On Thu, Nov 3, 2016 at 6:59 AM, paul <pcant...@gmail.com> wrote:
Hello,

When I executed IGV.sh with a batch script on a MacOS 10.10 inside of a PuTTY session, I get following error:

INFO [2016-11-03 09:54:42,099]  [DirectoryManager.java:149] [main]  IGV Directory: /Volumes/DataBackup/Share/refs/igv
INFO [2016-11-03 09:54:42,107]  [Main.java:82] [main]  Startup  IGV Version 2.3.26 (30)01/21/2014 10:36 AM
INFO [2016-11-03 09:54:42,126]  [Main.java:83] [main]  Java 1.7.0_76
Fetching user directory... INFO [2016-11-03 09:54:42,224]  [Main.java:84] [main]  Default User Directory: /Users/asdf
INFO [2016-11-03 09:54:42,225]  [Main.java:85] [main]  OS: Mac OS X
ERROR [2016-11-03 09:54:42,325]  [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:535)
        at java.awt.Frame.<init>(Frame.java:420)
        at java.awt.Frame.<init>(Frame.java:385)
        at javax.swing.JFrame.<init>(JFrame.java:180)
        at org.broad.igv.ui.Main.main(Main.java:64)



How do I fix this? Thank you,

Paul

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James Robinson

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Nov 4, 2016, 10:51:25 AM11/4/16
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Hi, no there is not,  IGV requires a display or a simulated display.   I know others have used Xvfb but I personally don't have any experience with it.    

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