again, have you tried running your Rscript outside of Galaxy called by Rscript_wrapper.sh ? To me, it looks like you have a bug in your Rscript and/or your wrapper. Hans-Rudolf 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'
On Mon, Apr 28, 2014 at 9:40 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto: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> <mailto: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
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