error while running Intogen.

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error while running Intogen.

do kadya

Respected Sir / Ma'am,

I was running Intogen using galaxy, I changes parameters name and then this error came.

Can you please tell what is the meaning of this error ?

Traceback (most recent call last):
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 123, in prepare_job
    job_wrapper.prepare()
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/tools/__init__.py", line 2639, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/home/ganit/galaxy_work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1395998029_86_91764.py", line 100, in respond
NotFound: cannot find 'fimpact'

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Re: error while running Intogen.

Jen Hillman-Jackson
Hello,

Do you mean that you modified the wrapper (py or xml) and now the tool is producing an error in your local Galaxy install?

When modifying a display label/variable, make sure it is consistent across all wrapper components. 

But modifying the syntax actually evolved as a parameter in the command line for any tool is bound to be problematic. You must use what the tool expects / see any tool's manual for the correct usage. 

Existing tools that function are good models for how to do this. For example, the tool shed will sometimes have alternate versions of wrappers for the same underlying tool - these will show you what can be variable and what must remain consistent.

If your question has been misunderstood, please send more details. You also probably want to post programming questions to the [hidden email] mailing list instead (development list). Searching that list for prior Q&A is also an option: http://galaxyproject.org -> MailingLists

thanks!

Jen
Galaxy Team

Jennifer Hillman-Jackson

On Mar 28, 2014, at 2:44 AM, do kadya <[hidden email]> wrote:


Respected Sir / Ma'am,

I was running Intogen using galaxy, I changes parameters name and then this error came.

Can you please tell what is the meaning of this error ?

Traceback (most recent call last):
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 123, in prepare_job
    job_wrapper.prepare()
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/jobs/__init__.py", line 702, in prepare
    self.command_line = self.tool.build_command_line( param_dict )
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/tools/__init__.py", line 2639, in build_command_line
    command_line = fill_template( self.command, context=param_dict )
  File "/home/ganit/galaxy_work/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
    return str( Template( source=template_text, searchList=[context] ) )
  File "/home/ganit/galaxy_work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "cheetah_DynamicallyCompiledCheetahTemplate_1395998029_86_91764.py", line 100, in respond
NotFound: cannot find 'fimpact'
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

 http://galaxyproject.org/search/mailinglists/

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org