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/
