Sure enough, this fixed the problem. I just installed the latest Sun JRE
and it is working now. Thanks for the suggestion! I would have never
guessed.

-Josh

On Mon, Jun 25, 2012 at 11:34 AM, simon andrews <
simon.andr...@babraham.ac.uk> wrote:

>  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.
>
>  Simon.
>
>  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*
> *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.andr...@babraham.ac.uk> 
> <galaxy-dev%40lists.bx.psu.edu?Subject=Re%3A%20%5Bgalaxy-dev%5D%20FastQC%20Tool%20Errors&In-Reply-To=%3CD9909700-8628-4478-814C-449803EE45F1%40babraham.ac.uk%3E>
>  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 <jniel...@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
>> >
>> >
>> > ___________________________________________________________
>> > Please keep all replies on the list by using "reply all"
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>> >  http://lists.bx.psu.edu/
>>
>>
>>
>> --
>> Ross Lazarus MBBS MPH;
>> Associate Professor, Harvard Medical School;
>> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>>
>
>
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