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.k...@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
>
>
>
>
>
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