Hi Rafi, 
Based on the error report, it looks like a problem with the template. Is the tool form rendering in the browser and the job is failing once you hit submit job or earlier?
Also, running from the command line that works - this is on the same amazon instance or your local instance?
Lastly, the path that keeps showing up (/nfs/sftware...) - is this something you have added and configured on your amazon instance or is this left over from your local deployment?

Enis

On Mon, Aug 1, 2011 at 1:38 AM, Faiaz Khan <faiaz.a.khan@gmail.com> wrote:
Hello,

I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: 

Traceback (most recent call last):
  File "/nfs/software/galaxy/lib/galaxy/jobs/runners/local.py", line 61, in run_job
    job_wrapper.prepare()
  File "/nfs/software/galaxy/lib/galaxy/jobs/__init__.py", line 371, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/nfs/software/galaxy/lib/galaxy/tools/__init__.py", line 1543, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/nfs/software/galaxy/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py", line 83, in respond
EOFError: EOF when reading a line

With the additional caption "failure to prepare job".
I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this?




Thanks,

Rafi




___________________________________________________________
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/