Thank you for your patience and help, I removed the periods and am running
into this error:

/bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat:
Permission denied

Does it have to do with the fact Im using SQLite and not Postgres?


On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:

> Hi Bradley,
>
> For your inputs, don’t use periods (‘.’) within the param names.
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Apr 29, 2014, at 12:32 PM, Bradley Belfiore <bradbelf2...@gmail.com>
> wrote:
>
> The XML file is:
> <tool id="pathview" name="pathview" version="1.0">
> <description> Pathview is a tool set for pathway based data integration
> and visualization. It maps and renders a wide variety of biological data
> on relevant pathway graphs.</description>
> <command> interpreter="Rscript">
> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $
> pathway.id $species $out.suffix $output </command>
> <inputs>
> <param name="gene.data" type="data" format="data" label="enter input
> file"/>
> <param name="pathway.id" type="text" format="text" label="Pathway ID"/>
>  <param name="species" type="text" format="text" label="Species"/>
> <param name="out.suffix" type="text" format="text" label="Output Suffix" />
> </inputs>
> <outputs>
>    <data format="pdf" name="output"/>
> </outputs>
> </tool>
>
> With basic Rscript :
> args <- commandArgs(TRUE)
> ## inputs
> gene.data <- args[1]
> pathway.id <- args[2]
> species <-args[3]
> out.suffix <-args[4]
> output <-args[5]
>
> suppressMessages(library("pathview"))
> suppressMessages(library("KEGGgraph"))
> suppressMessages(library("Rgraphviz"))
>
> pv.out <- pathview(gene.data=gene.data , pathway.id= pathway.id,
> species=species, out.suffix=output, kegg.native=T)
>
>
> On Tue, Apr 29, 2014 at 12:26 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
>> Hi Brad
>>
>> To me, this looks like an error in tool definition file (ie the xml
>> file). Something like using $gene in the "command" tag without defining it
>> in a "param" tag. But it is difficult to guess without seeing to full xml
>> file.
>>
>>
>> Regards Hans-Rudolf
>>
>>
>> On 04/29/2014 06:13 PM, Bradley Belfiore wrote:
>>
>>> Upon  going back over my script I got it working on the command line as
>>> suggested, and when attempting to execute in my instance of galaxy I got
>>> this error message which I was not sure about:
>>>
>>> Traceback (most recent call last):
>>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>>> line 152, in prepare_job
>>>      job_wrapper.prepare()
>>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line
>>> 701, in prepare
>>>      self.command_line = self.tool.build_command_line( param_dict )
>>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/tools/__init__.py",
>>> line 2773, in build_command_line
>>>      command_line = fill_template( self.command, context=param_dict )
>>>    File "/Users/bbelfio1/galaxy-dist/lib/galaxy/util/template.py", line
>>> 9, in fill_template
>>>      return str( Template( source=template_text, searchList=[context] ) )
>>>    File "/Users/bbelfio1/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-
>>> macosx-10.6-intel-ucs2.egg/Cheetah/Template.py", line 1004, in __str__
>>>      return getattr(self, mainMethName)()
>>>    File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
>>> NotFound: cannot find 'gene'
>>>
>>>
>>>
>>> On Mon, Apr 28, 2014 at 12:07 PM, Hans-Rudolf Hotz <h...@fmi.ch
>>> <mailto:h...@fmi.ch>> wrote:
>>>
>>>     Hi Brad
>>>
>>>
>>>
>>>     On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
>>>
>>>         So upon doing what you suggested, I get:
>>>
>>>         bravo:galaxy-dist bbelfio1$ 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>
>>>         <http://pathway.id>) :
>>>
>>>             argument "pathway.id <http://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>
>>>         <mailto: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>>
>>>                  <mailto:p.j.a.cock@googlemail.
>>>         <mailto:p.j.a.cock@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>>
>>>                       <mailto: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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