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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