Yes when running in command line I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R Error in value[[3L]](cond) : failed to read experimental design data: cannot open the connection Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
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