Tool: rnastar in galaxy
0
gravatar for b.roux
4.7 years ago by
b.roux0
United Kingdom
b.roux0 wrote:

Hi all

I'm trying to run rnastar form my galaxy local. I've downloaded rnastar from the test toolshed and when I executed it I got an error message: 

failure preparing job

and for more details:

Traceback (most recent call last):
  File "/Users/br237/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 157, in prepare_job
    job_wrapper.prepare()
  File "/Users/br237/galaxy-dist/lib/galaxy/jobs/__init__.py", line 828, in prepare
    self.command_line, self.extra_filenames = tool_evaluator.build()
  File "/Users/br237/galaxy-dist/lib/galaxy/tools/evaluation.py", line 371, in build
    self.__build_command_line( )
  File "/Users/br237/galaxy-dist/lib/galaxy/tools/evaluation.py", line 387, in __build_command_line
    command_line = fill_template( command, context=param_dict )
  File "/Users/br237/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/Users/br237/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1425642260_92_41633.py", line 112, in respond
  File "/Users/br237/galaxy-dist/lib/galaxy/tools/wrappers.py", line 122, in __getattr__
    self._fields[ name ] = self._input.options.get_field_by_name_for_value( name, self._value, None, self._other_values )
  File "/Users/br237/galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py", line 578, in get_field_by_name_for_value
    assert field_name in self.columns, "Requested '%s' column missing from column def" % field_name
AssertionError: Requested 'pathls' column missing from column def

Any thoughts on that?

Thanks for your help

tool alignment • 1.3k views
ADD COMMENTlink modified 4.7 years ago by Biomonika (Noolean)3.1k • written 4.7 years ago by b.roux0
0
gravatar for Biomonika (Noolean)
4.7 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

This would be better place to ask:

https://biostar.usegalaxy.org/

ADD COMMENTlink written 4.7 years ago by Biomonika (Noolean)3.1k

Thanks, I haven't realised that there were two different forum.

ADD REPLYlink written 4.7 years ago by b.roux0
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