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" >> > in your mail client. To manage your subscriptions to this >> > and other Galaxy lists, please use the interface at: >> > >> > http://lists.bx.psu.edu/ >> >> >> >> -- >> 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.* > > 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: > www.babraham.ac.uk<http://www.babraham.ac.uk/email_disclaimer.html> >
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