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 <h...@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 <h...@fmi.ch
>> <mailto:h...@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"
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>>
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>>
>>
>>
___________________________________________________________
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