Kristen Eisenberg wrote: > [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?
Hi Kristen, Could you post the relevant XML file to the list? The error unfortunately indicates a syntax error or typo. --nate > > Kristen Eisenberg > Billige Flüge > Marketing GmbH > Emanuelstr. 3, > 10317 Berlin > Deutschland > Telefon: +49 (33) > 5310967 > Email: > utebachmeier at gmail.com > Site: > http://flug.airego.de - Billige Flüge vergleichen > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
