Yes, that's the broken version of gcj.  I don't have a Centos machine 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 things.


On 25 Jun 2012, at 17:19, Josh Nielsen wrote:

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

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


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 
<<>> 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(
> at java.awt.Window.<init>(
> at java.awt.Frame.<init>(
> at java.awt.Frame.<init>(
> at javax.swing.JFrame.<init>(
> 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). 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
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:

Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 

The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered 
Charity No. 1053902.
The information transmitted in this email is directed only to the addressee. If 
you received this in error, please contact the sender and delete this email 
from your system. The contents of this e-mail are the views of the sender and 
do not necessarily represent the views of the Babraham Institute. Full 
conditions at:<>
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

Reply via email to