Thanks Simon! I'll definitely give that a shot.
On Mon, Jun 25, 2012 at 11:34 AM, simon andrews <
Yes, that's the broken version of gcj. I don't have a
here at the moment, but I think if you install OpenJDK and use the
alternatives system to select that as the default JRE then that should fix
On 25 Jun 2012, at 17:19, Josh Nielsen wrote:
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
*warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
Is this version of Java too old? Perhaps I need to install the JRE
On *Sat Jun 23 04:20:53 EDT 2012*, Simon Andrews <
> 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).
> On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen <jnielsen(a)hudsonalpha.com>
> > 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,
> > 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
> > 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
> > 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
> > at
> > 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).
> > this application is GUI-driven how did the online PSU Galaxy get it to
> > 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
> > I'm missing here to getting this to work with our Galaxy mirror, other
> > 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;
The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT *Registered
Charity No. 1053902.*
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