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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