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