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
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
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
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
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
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
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
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
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
