Re: [galaxy-dev] FastQC Tool Errors

[Robert Chase]

Hello,

We are having trouble running FastQC on our production server.

The original stacktrace looked like this;

Fastq failed.
Error executing FastQC. Unknown option: djava.awt.headless
Exception in thread "main" java.lang.NoClassDefFoundError:
uk/ac/bbsrc/babraham/FastQC/FastQCApplication
Caused by: java.lang.ClassNotFoundException:
uk.ac.bbsrc.babraham.FastQC.FastQCApplication
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Could not find the main class:
uk.ac.bbsrc.babraham.FastQC.FastQCApplication.  Program will exit.

Then I tried to update java to the most current version. The current
version is

java -version
java version "1.7.0_05"
Java(TM) SE Runtime Environment (build 1.7.0_05-b06)
Java HotSpot(TM) 64-Bit Server VM (build 23.1-b03, mixed mode)

This changed the error message we got when we ran FastQC. The new trace
looks like this;

Fastq failed.
Error executing FastQC. Unknown option: djava.awt.headless
Error: Could not find or load main class
uk.ac.bbsrc.babraham.FastQC.FastQCApplication

The strange thing is that the tools works on our test server, which is
almost an exact copy of the production server.

-Rob

__

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 <[hidden
email]
> 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 <[hidden
email]
 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 <[hidden 
> email]>
> 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.(Window.java:437)
> > at java.awt.Frame.(Frame.java:419)
> > at java.awt.Frame.(Frame.java:384)
> > at javax.swing.JFrame.(JFrame.java:174)
> > at
> >
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(FastQCApplication.java:271)
> > at
> >
> uk.ac.bbsrc.babraham.FastQC.FastQCApplicat

Re: [galaxy-dev] FastQC Tool Errors

[Josh Nielsen]

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> 
> 
>  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 
>> 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.(Window.java:437)
>> > at java.awt.Frame.(Frame.java:419)
>> > at java.awt.Frame.(Frame.java:384)
>> > at javax.swing.JFrame.(JFrame.java:174)
>> > at
>> >
>> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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
>
___
Please keep all replies on the list by using "reply all"
in 

Re: [galaxy-dev] FastQC Tool Errors

[simon andrews]

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  

  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 
mailto: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.(Window.java:437)
> at java.awt.Frame.(Frame.java:419)
> at java.awt.Frame.(Frame.java:384)
> at javax.swing.JFrame.(JFrame.java:174)
> at
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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
___
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/

Re: [galaxy-dev] FastQC Tool Errors

[Josh Nielsen]

Thanks Simon! I'll definitely give that a shot.

-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> 
> 
>  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 
>> 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.(Window.java:437)
>> > at java.awt.Frame.(Frame.java:419)
>> > at java.awt.Frame.(Frame.java:384)
>> > at javax.swing.JFrame.(JFrame.java:174)
>> > at
>> >
>> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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
>
___
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 interfac

Re: [galaxy-dev] FastQC Tool Errors

[Josh Nielsen]

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>

 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 
> 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.(Window.java:437)
> > at java.awt.Frame.(Frame.java:419)
> > at java.awt.Frame.(Frame.java:384)
> > at javax.swing.JFrame.(JFrame.java:174)
> > at
> >
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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/

Re: [galaxy-dev] FastQC Tool Errors

[Josh Nielsen]

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  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 
> 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.(Window.java:437)
> > at java.awt.Frame.(Frame.java:419)
> > at java.awt.Frame.(Frame.java:384)
> > at javax.swing.JFrame.(JFrame.java:174)
> > at
> >
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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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Re: [galaxy-dev] FastQC Tool Errors

[simon andrews]

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 22 Jun 2012, at 23:35, Ross 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  
> 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.(Window.java:437)
>> at java.awt.Frame.(Frame.java:419)
>> at java.awt.Frame.(Frame.java:384)
>> at javax.swing.JFrame.(JFrame.java:174)
>> at
>> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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/

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Re: [galaxy-dev] FastQC Tool Errors

[Ross]

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  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.(Window.java:437)
> at java.awt.Frame.(Frame.java:419)
> at java.awt.Frame.(Frame.java:384)
> at javax.swing.JFrame.(JFrame.java:174)
> at
> uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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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[galaxy-dev] FastQC Tool Errors

[Josh Nielsen]

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.(Window.java:437)
at java.awt.Frame.(Frame.java:419)
at java.awt.Frame.(Frame.java:384)
at javax.swing.JFrame.(JFrame.java:174)
at
uk.ac.bbsrc.babraham.FastQC.FastQCApplication.(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
___
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