We are not currently running anything like Xvfb, but if that is the only way to get it to run I suppose I can try it. How does PSU's Galaxy handle grabbing the results and outputting them to Galaxy without having X11 applications (useless/unneeded with Galaxy - meant for manual thickclient GUI interaction not browsers) starting on the servers on their end for every user job executed? And how do they kill or manage the opened X11 sessions once started? The users do not/aren't supposed to see the X11 / R Graphics, correct? They are only supposed to see whatever file output it results in so that they can view it strictly through Galaxy, as per the wrapper's text description: "The tool produces a single HTML output file that contains all of the results". It is only the results summary in HTML that Galaxy & the user are concerned about, as I understand it.
We run Galaxy on a Linux cluster headnode (with no monitor & only boots to init 3 [no GUI] - with admin-only ssh access) and it submits all jobs to the compute nodes and then returns the results. I installed Java on each compute nodes but do I now need to install that X11 virtual frame buffer/Xvfb on all of the compute nodes also? Thanks! On Fri, Jun 22, 2012 at 5:35 PM, Ross <ross.laza...@gmail.com> wrote: > Do you run an X11 virtual frame buffer - eg Xvfb? > Otherwise AFAIK R graphics and Java will complain on headless nodes. > > 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; >
___________________________________________________________ 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/