This is not what I suggested, I said

Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output

replacing $genedata $pathwayid $species $output with meaningful arguments

On 04/28/2014 04:29 PM, Bradley Belfiore wrote:

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

<mailto: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

    <mailto: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