So upon doing what you suggested, I get: bravo:galaxy-dist bbelfio1$ Rscript /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R '/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA' Error in grep(species, pathway.id) : argument "pathway.id" is missing, with no default Calls: pathview -> grep Execution halted On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
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