Hello,

I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output:

"Started analysis of Clip

Approx 5% complete for Clip
Approx 10% complete for Clip
...
...
Approx 95% complete for Clip
Approx 100% complete for Clip

Analysis complete for Clip

(.:9754): Gtk-WARNING **: cannot open display: "

And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this:

"Exception in thread "main" 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:173)
at java.awt.Window.<init>(Window.java:437)
at java.awt.Frame.<init>(Frame.java:419)
at java.awt.Frame.<init>(Frame.java:384)
at javax.swing.JFrame.<init>(JFrame.java:174)
at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:271)
at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102)"

Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions?

Thanks,
Josh