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; >
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