Re: [galaxy-dev] Failure to prepare job error
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 Torsten Schwab Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: woozydude@gmail.com Site: http://flug.prexxis.de/
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 Telefon: +49 (33) 5310967 Email: woozydude@gmail.com Site: http://flug.prexxis.de/ ___________________________________________________________ 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:
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Nate Coraor -
Woozy