Hi,

I created a metadata (“config”) and want to run my tool using that.

I am getting this error when I try to use the uploaded file with this new extension .

I have specified the command line parameters as :

<command interpreter="bash">kelvin_wrapper $confile  ${os.path.join( confile.extra_files_path , 'pedfile.txt' )}  ${os.path.join( confile.extra_files_path , 'mapfile.txt')}  ${os.path.join( confile.extra_files_path , 'frequencyfile.txt' )} ${os.path.join( confile.extra_files_path , 'datafile.txt')} $brfile $pplfile $modfile</command>

Error:

Traceback (most recent call last):
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py", line 120, in queue_job
    job_wrapper.prepare()
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 390, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 1343, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1275498667_76_83196.py", line 86, in respond
NameError: global name 'confile' is not defined
Tool execution generated the following error message:
failure preparing job


Can anybody please help

Regards,
Amit Modi

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