Thank you James, i was able to add up the button next to Run Workflow as i wished. I also found out the run script which is if 'run_workflow' in kwargs and not errors: # Run each step, connecting outputs to inputs 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 ) return trans.fill_template( "workflow/run_complete.mako", workflow=stored, outputs=outputs ) How can I extract the command line arguments for the tools that have been used in this workflow. It is the same as seen in jobs table in the database like for Add_a_column1 it is python /home/raghav/Desktop/myGalaxy/tools/stats/column_maker.py /home/raghav/Desktop/myGalaxy/database/files/000/dataset_38.dat /home/raghav/Desktop/myGalaxy/database/files/000/dataset_39.dat "c3-c2" no 6 "str,int,int,str,int,str" Also how do I get the list of all the dummy Dataset that has been created by the workflow? So I was wondering somehow this command is being issued by the RUN button itself. I just want the list of all such commands. Can you please tell me how can I get it? Regards, On Thu, Dec 3, 2009 at 6:24 AM, James Taylor <james@bx.psu.edu> wrote:

If you give us a little more information on what you want to do I imagine we can help more, I'm not sure I completely understand. However, for your specific questions:

- Running a workflow creates a set of jobs which are linked through a set of datasets [actually history_dataset_association rows, an HDA is basically a users personal view of a dataset]. For example, job1 -> job_to_output_dataset_assoc -> history_dataset_assoc -> job_to_input_dataset_assoc -> job2 means that job2 must complete before job2 can run.

- When you click run workflow, the request is handled by the run method in the workflow controller (galaxy.web.controllers.workflow)

- You'll need to edit the mako templates directly for this, they are in the directory templates. If you look at the controller method you are interested in, at some point it will call "fill_template", which tells you exactly what template file you need to look at.

On Dec 3, 2009, at 3:52 AM, Raghav Bhatnagar wrote:

Hi Team

...

I have successfully transformed the Workflow that is created by Galaxy into another system that does very much the same thing. Now I need to integrate it to the galaxy Interface. I want a button beside "Run Workflow" which would enable user to Run the same workflow into another system.

1.) One thing I wanted to know that it relates to the database using "job_to_input_dataset" and "history_dataset_association" when we Click on Run Workflow. Where can I find the code for the "Run Workflow" Button? Since the same logic has to be applied to that too in order to make it consistent.

2.) I know how to add tools to Galaxy but How do I add a "Run Workflow using xxx" button beside "Run Workflow" in Galaxy Interface?

Regards,

-- Raghav Bhatnagar Graduate Student (CS) Viterbi School of Engineering University of Southern California _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

-- Raghav Bhatnagar Graduate Student (CS) Viterbi School of Engineering University of Southern California