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