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_... Thanks, Carlos On Tue, Nov 8, 2011 at 4:31 PM, Daniel Blankenberg <dan@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.borroto@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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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 <dan@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_.... 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_...

Thanks, Carlos

On Tue, Nov 8, 2011 at 4:31 PM, Daniel Blankenberg <dan@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.borroto@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'

___________________________________________________________

Please keep all replies on the list by using "reply all"

in your mail client.  To manage your subscriptions to this

and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/