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
   File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/__init__.py", line 701, in 
     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 
     return str( Template( source=template_text, searchList=[context] ) )
 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/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:

        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


        On Mon, Apr 28, 2014 at 10:35 AM, Hans-Rudolf Hotz <h...@fmi.ch
        <mailto:h...@fmi.ch <mailto:h...@fmi.ch>>> wrote:

             This is not what I suggested, I said


             $pathwayid $species $output

             replacing $genedata $pathwayid $species $output with meaningful

             On 04/28/2014 04:29 PM, Bradley Belfiore wrote:

                 Yes when running in command line I get:

                 bravo:galaxy-dist bbelfio1$ Rscript

                 Error in value[[3L]](cond) :

                     failed to read experimental design data: cannot
        open the

                 Calls: tryCatch -> tryCatchList -> tryCatchOne ->

                 In addition: Warning message:

                 In file(file, "rt") : cannot open file 'NA': No such
        file or

                 Execution halted

                 On Mon, Apr 28, 2014 at 10:19 AM, Peter Cock

        <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

                       >> line 153, in prepare_job
                       >>      job_wrapper.runner_command_____line =
                       >> job_wrapper,
        include_work_dir_outputs=____include_work_dir_outputs )
                       >>    File


                       >> 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


                       >> line 19, in build_command
                       >>      commands_builder =
                       >>    File


                       >> 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>>>> 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.



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