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'


On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
"Please keep all replies on the list by using "reply all""


well, what happens if you run


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

on the command line yourself (or rather as the user galaxy is running as), replacing $genedata $pathwayid $species $output with meaningful arguments


Hans-Rudolf





On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
Thank you for your quick response, my command tag is:
<command>
interpreter="bash">Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
</command>

So I believe Im calling R via the Rscript_wrapper.sh?

As far as the #!/bin/bash, not sure why I had that there, I took it out now.
thanks,
Bradley Belfiore


On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz <hrh@fmi.ch
<mailto:hrh@fmi.ch>> wrote:

    Hi Brad

    I don't you are using R to execute your R script....

    How do you call your R script, ie how does the command tag looks in
    the tool definition file?

    Also, why do you have a "#!/bin/bash" at the beginning of your R script?


    Regards, Hans-Rudolf




    On 04/27/2014 09:50 PM, Bradley Belfiore wrote:

        I am new to galaxy and while trying to convert an R tool to a Galaxy
        usable tool I keep  getting:
        /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:

        syntax
        error near unexpected token `('

        /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1:

        `args=(commandArgs(TRUE))'


        any help as to how to remedy this would be greatly appreciated.  The
        first couple lines of my .R file are
        #
        #!/bin/bash
        args<-(commandArgs(TRUE))

        Thanks,
        Brad


        _____________________________________________________________

        Please keep all replies on the list by using "reply all"
        in your mail client.  To manage your subscriptions to this
        and other Galaxy lists, please use the interface at:
        http://lists.bx.psu.edu/

        To search Galaxy mailing lists use the unified search at:
        http://galaxyproject.org/__search/mailinglists/
        <http://galaxyproject.org/search/mailinglists/>