> On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
>>
>> The initial error now seems to be taken care of and now am getting this
>> message on attempting to run tool:
>>
>> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>> line 153, in prepare_job
>>      job_wrapper.runner_command_line = self.build_command_line(
>> job_wrapper, include_metadata=include_metadata,
>> include_work_dir_outputs=include_work_dir_outputs )
>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>> line 176, in build_command_line
>>      return build_command( self, job_wrapper,
>> include_metadata=include_metadata,
>> include_work_dir_outputs=include_work_dir_outputs )
>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
>> line 19, in build_command
>>      commands_builder = CommandsBuilder(job_wrapper.get_command_line())
>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/command_factory.py",
>> line 109, in __init__
>>      commands = initial_command.rstrip("; ")
>> AttributeError: 'NoneType' object has no attribute 'rstrip'
>>

This is still breaking inside Galaxy, before ever trying to run your
scripts. There is likely still a problem in your XML.

On Mon, Apr 28, 2014 at 3:08 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
> again, have you tried running your Rscript outside of Galaxy called by
> Rscript_wrapper.sh ?
>

This is an important question :)

Also, please remember to CC the mailing list and not just reply
to the previous email's sender only.

Thanks,

Peter