How to extract Job List
Hi Galaxy Team I have been working to extract the job list before it is executed into Galaxy. I came to knwo that when we press the Run Workflow button, the following code is executed. Can you please let me know which line inserts code into the jobs table and how do I find that? outputs = odict() for i, step in enumerate( workflow.steps ): if step.type == 'tool' or step.type is None: tool = trans.app.toolbox.tools_by_id[ step.tool_id ] input_values = step.state.inputs # Connect up def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): if prefixed_name in step.input_connections_by_name: conn = step.input_connections_by_name[ prefixed_name ] return outputs[ conn.output_step.id ][ conn.output_name ] visit_input_values( tool.inputs, step.state.inputs, callback ) # Execute it outputs[ step.id ] = tool.execute( trans, step.state.inputs ) else: outputs[ step.id ] = step.module.execute( trans, step.state ) -- Raghav Bhatnagar Graduate Student (CS) Viterbi School of Engineering University of Southern California
Thank you for a quick reply. Is it possible to extract the dataset names and jobs without it being exeuted in galaxy? I suppose tool.execute creates the datasets and jobs and execute it. On Tue, Dec 8, 2009 at 12:53 PM, James Taylor <james@bx.psu.edu> wrote:
The job is created by tool.execute, you probably want to look at DefaultToolAction where datasets and jobs are actually created.
On Dec 8, 2009, at 3:50 PM, Raghav Bhatnagar wrote:
outputs[ step.id ] = tool.execute( trans,
step.state.inputs )
-- Raghav Bhatnagar Graduate Student (CS) Viterbi School of Engineering University of Southern California
participants (2)
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James Taylor
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Raghav Bhatnagar