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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