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.andrews@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.andrews@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 <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
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
component of than
just dropping the executable in place? Any suggestions?
Thanks, Josh
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