Hi Dan,

Thanks for your response, but I'm still confused.

When I edit the workflow there are two different kind of "Reference
genome" fields. One where I can use a drop down menu to select a
reference genome, like in "Unified Genotyper" tool, where you are
correct the only option is hg_g1k_v37 in the public server, but I
don't have any trouble with it, as I can choose whether or not to set
ahead and I don't get any error in any case. There is another kind of
field where there is only a text box, like in "Indel Realigner" or
"Count Covariates" tools, this is the one giving me trouble. Here if I
choose to set during runtime I get the error I commented before, if I
leave it blank what I get at runtime is this text "None (value not yet
validated)", thus my confusion.

And finally I can't find in these tools documentation, "Indel
Realigner" or "Count Covariates", anything about a reference genome
argument, is this field just for annotation purpose?
http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_walkers_recalibration_CountCovariatesWalker.html

Thanks,
Carlos

On Tue, Nov 8, 2011 at 4:31 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi Carlos,
>
> This is a known bug with running workflows and we are working on a fix.  
> Thanks for reporting this error.
>
> The current work-around is to set the reference genome value in the select 
> boxes (currently only 'hg_g1k_v37' is available on our public server) 
> directly within the workflow editor, or to use a reference genome from your 
> history.
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Nov 8, 2011, at 3:42 PM, Carlos Borroto wrote:
>
>> I was able to make the error disappear. By trial and error I found the
>> error appear when I set any tool with "Using reference genome" as "To
>> be set at runtime". But only for tools which don't display a drop down
>> menu to select a reference.
>>
>> I'm confuse by this, I'm guessing these tools will take the reference
>> value set before by another tool. Still I think there is a bug here.
>>
>> Thanks,
>> Carlos
>>
>> On Tue, Nov 8, 2011 at 3:03 PM, Carlos Borroto <carlos.borr...@gmail.com> 
>> wrote:
>>> Hi,
>>>
>>> I'm trying to develop a workflow using several tools from GATK and
>>> Picard sections among others. I'm able to run all the tools and from
>>> the history I'm creating a workflow, but I'm running into an error. I
>>> have copied the full debugging trace from my local Galaxy, I was able
>>> to import this workflow into the test server and here it is:
>>> http://test.g2.bx.psu.edu/u/cjav/w/gatk---unified-genotyper
>>>
>>> The test server also gave me an error, but I don't have the option to
>>> see the debugging trace.
>>>
>>> Thanks a lot for any help,
>>> Carlos
>>>
>>> URL: http://localhost:8888/workflow/run?id=f597429621d6eb2b
>>> File 
>>> '/home/cborroto/galaxy_dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
>>> line 364 in respond
>>>  app_iter = self.application(environ, detect_start_response)
>>> File 
>>> '/home/cborroto/galaxy_env/lib/python2.7/site-packages/paste/debug/prints.py',
>>> line 106 in __call__
>>>  environ, self.app)
>>> File 
>>> '/home/cborroto/galaxy_env/lib/python2.7/site-packages/paste/wsgilib.py',
>>> line 543 in intercept_output
>>>  app_iter = application(environ, replacement_start_response)
>>> File 
>>> '/home/cborroto/galaxy_env/lib/python2.7/site-packages/paste/recursive.py',
>>> line 84 in __call__
>>>  return self.application(environ, start_response)
>>> File 
>>> '/home/cborroto/galaxy_env/lib/python2.7/site-packages/paste/httpexceptions.py',
>>> line 633 in __call__
>>>  return self.application(environ, start_response)
>>> File '/home/cborroto/galaxy_dist/lib/galaxy/web/framework/base.py',
>>> line 145 in __call__
>>>  body = method( trans, **kwargs )
>>> File '/home/cborroto/galaxy_dist/lib/galaxy/web/controllers/workflow.py',
>>> line 1438 in run
>>>  incoming=kwargs )
>>> File '/home/cborroto/galaxy_dist/lib/galaxy/web/framework/__init__.py',
>>> line 691 in fill_template
>>>  return self.fill_template_mako( filename, **kwargs )
>>> File '/home/cborroto/galaxy_dist/lib/galaxy/web/framework/__init__.py',
>>> line 702 in fill_template_mako
>>>  return template.render( **data )
>>> File 
>>> '/home/cborroto/galaxy_dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
>>> line 296 in render
>>>  return runtime._render(self, self.callable_, args, data)
>>> File '/home/cborroto/galaxy_dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
>>> line 660 in _render
>>>  **_kwargs_for_callable(callable_, data))
>>> File '/home/cborroto/galaxy_dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
>>> line 692 in _render_context
>>>  _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
>>> File '/home/cborroto/galaxy_dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
>>> line 718 in _exec_template
>>>  callable_(context, *args, **kwargs)
>>> File '/home/cborroto/galaxy_dist/database/compiled_templates/base.mako.py',
>>> line 42 in render_body
>>>  __M_writer(unicode(next.body()))
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 160 in render_body
>>>  __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs,
>>> errors.get( step.id, dict() ), "", step )))
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 40 in do_inputs
>>>  return 
>>> render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values)
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 406 in render_do_inputs
>>>  __M_writer(unicode(do_inputs( input.cases[ current_case ].inputs,
>>> group_values, group_errors, new_prefix, step, other_values )))
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 317 in do_inputs
>>>  return 
>>> render_do_inputs(context,inputs,values,errors,prefix,step,other_values)
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 412 in render_do_inputs
>>>  __M_writer(unicode(row_for_param( input, values[ input.name ],
>>> other_values, errors, prefix, step )))
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 315 in row_for_param
>>>  return 
>>> render_row_for_param(context,param,value,other_values,error_dict,prefix,step)
>>> File 
>>> '/home/cborroto/galaxy_dist/database/compiled_templates/workflow/run.mako.py',
>>> line 503 in render_row_for_param
>>>  value = other_values[ param.name ] = param.get_initial_value( t,
>>> other_values )
>>> File '/home/cborroto/galaxy_dist/lib/galaxy/tools/parameters/basic.py',
>>> line 762 in get_initial_value
>>>  if self.need_late_validation( trans, context ):
>>> File '/home/cborroto/galaxy_dist/lib/galaxy/tools/parameters/basic.py',
>>> line 745 in need_late_validation
>>>  dep_value = context[ dep_name ]
>>> KeyError: 'input_bam'
>>>
>>
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>
>

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