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" >> 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/> >> >> >>
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