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s-andrews / FastQC

A quality control analysis tool for high throughput sequencing data
GNU General Public License v3.0
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another "Headless exception" problem #98

Closed dsb66 closed 1 year ago

dsb66 commented 2 years ago

I am trying to run FastQC in interactive mode on a remote RedHat server that runs the standard Gnome desktop. Session and error message:

`(base) FastQC$ ./fastqc

Exception in thread "main" java.awt.HeadlessException at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204) at java.awt.Window.(Window.java:536) at java.awt.Frame.(Frame.java:420) at java.awt.Frame.(Frame.java:385) at javax.swing.JFrame.(JFrame.java:189) at uk.ac.babraham.FastQC.FastQCApplication.(FastQCApplication.java:63) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:338) ` This used to work on remote Ubuntu desktop. I am connecting to the RedHat server through a tunneled VNC connection. I don't want to do X11 forwarding and would prefer using the graphical interface. Please advise, thanks.

s-andrews commented 2 years ago

If you're on a VNC desktop then it should just work - we run all of our training desktops this way without issue. That error suggests that something isn't right in your connection as it's not finding a display to connect to, which would either be X to a VNC desktop, or an X tunnel back to a local X server. I'm guessing this problem would affect all graphical applications, not just fastqc so it's not really an issue with the setup of this program.

Without more details of how you've set up your connection I can't really suggest how to debug this, but there's certainly nothing within the program which would prevent this from working and we know that a similar setup works just fine on other systems so this should work.