Thanks a lot for your time!, I get it now and I should be able to run
my workflow.

On Wed, Nov 9, 2011 at 11:13 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi Carlos,
> In the cases where the Editor is showing a text box instead of the dropdown,
> you enter the unique id from the .loc file, in the case of the public Galaxy
> server this would be 'hg_g1k_v37', in the case of your local instance, this
> would be the id that you have assigned; this text box appears as a dropdown
> when running the tool interactively in the Galaxy interface (the dynamic
> nature of this select field -- filtered by dbkey of input -- is why it is
> displayed as a text field). These fields are what are causing a known bug
> with running the workflows with set at runtime, on which we are working on a
> fix, if you fill the text box to be hard set to the id from the .loc file,
> you can run the workflow.
> If you look at the example of Count Covariates on the page that you
> reference, you will see the reference genome specified as '-R
> resources/Homo_sapiens_assembly18.fasta'; this parameter is a standard GATK
> command line argument:
> http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_CommandLineGATK.html.
> Please let us know if we can provide additional information.
> Thanks for using Galaxy,
> Dan
>
> On Nov 9, 2011, at 11:01 AM, Carlos Borroto wrote:
>
> 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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