Woozy 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?

Hi Rafi,

Could you post your tool configuration to the list?

Thanks,
--nate

> 
> Thanks,
> 
> Rafi
> 
> 
> Torsten Schwab
> Marketing GmbH
> Emanuelstr. 3,
> 10317 Berlin
> Deutschland
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> Email: woozyd...@gmail.com
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