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