Hi Simon,

I recently installed Java with the yum package manager on our compute nodes, and our cluster is a Centos 6 environment. Here is what the results of "java -version" returned on the compute nodes:

"bash# java -version

java version "1.5.0"

gij (GNU libgcj) version 4.4.4 20100726 (Red Hat 4.4.4-13)

Copyright (C) 2007 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."

Is this version of Java too old? Perhaps I need to install the JRE manually?

Thanks!

On Sat Jun 23 04:20:53 EDT 2012, Simon Andrews <simon.andrews@babraham.ac.uk>  wrote:

Are you by any chance running an older version of gcj as your java version?  There is a known bug in some of these where they don't correctly configure the headless environment, even if the correct parameters are passed.  This causes exactly the kind of errors you're seeing.

If this is the case you'll need to install a more recent JRE (or update your path to point to one which is already present).

Simon.

On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen <jnielsen@hudsonalpha.com> wrote:
> 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
>
>
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;