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