Upon going back over my script I got it working on the command line as
suggested, and when attempting to execute in my instance of galaxy I got
this error message which I was not sure about:
Traceback (most recent call last):
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 152, in prepare_job
job_wrapper.prepare()
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line
701, in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py",
line 2773, in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line
9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
"/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-macosx-10.6-intel-ucs2.egg/Cheetah/Template.py",
line 1004, in __str__
return getattr(self, mainMethName)()
File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
NotFound: cannot find 'gene'
On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
> Hi Brad
>
>
>
> On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
>
>> 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'
>>
>>
> I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-....."
>
> I don't see the word "Rscript_wrapper.sh" in your line, hence it does not
> correspond to the command galaxy is executing
>
> You provide 3 arguments '/Users/bbelfio1/Documents/sample.txt', '04110',
> and 'HSA'
>
> However in an earlier mail you mention four arguments:
> $genedata
> $pathwayid
> $species
> $output
>
> Error in grep(species, pathway.id <http://pathway.id>) :
>>
>> argument "pathway.id <http://pathway.id>" is missing, with no default
>>
>>
>> Calls: pathview -> grep
>>
>> Execution halted
>>
>>
>>
> As long as you are not sure, whether your script is working on the command
> line the way you want it to be executed in Galaxy, there is no point in
> putting it into Galaxy
>
>
> Hans-Rudolf
>
>
>
>>
>> On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <h...@fmi.ch
>> <mailto:h...@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.c...@googlemail.com <mailto:p.j.a.c...@googlemail.com>
>> <mailto:p.j.a.cock@googlemail.__com
>>
>> <mailto:p.j.a.c...@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
>> <h...@fmi.ch <mailto:h...@fmi.ch>
>> <mailto:h...@fmi.ch <mailto:h...@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
>>
>>
>>
>>
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