Hi Craig,

Thanks for your interest in the galaxy API. For the parameters you're uncertain about:

The 'workflow_id' is indeed the encoded workflow id. You can get this by encoding it yourself, or doing a GET on /api/workflows for a list of *all* workflows and their encoded id's (see example below) The 'history' is either a name for a new history to be created, or a string of the format "hist_id=<encoded history_id to use>", if you have an existing history that you'd like the results to appear in. And the last parameter is a three part string. The first part is the step that the input should be mapped to, the second part is the *type* of input it is, and the third step is the actual encoded id. The type is going to be either ldda for a library dataset, or hda for a history dataset.

All of these encoded id's are discoverable through the API itself. Try using scripts/api/display.py to view /api/workflows, /api/workflows/<encoded_workflow_id> to get a feel for what's available to you.

Lastly, an example of how the run_workflow component of the api could be used as a part of an external pipeline can be found in scripts/api/example_watch_folder.py. This script monitors a particular folder for files, uploads them to galaxy, and executes a workflow on them.

Hope this helps, and definitely let me know if I can answer any more questions or if you have feedback about the API.

-Dannon

On Dec 1, 2011, at 7:32 PM, Craig Blackhart wrote:

I am newish to Galaxy and trying to learn how I might integrate it with our workflows and LIMS for automated data handling. I am aware of the API and have looked up all the documentation that I could find. However, there are many things I cannot make sense of, and have not been able to find information to help me out. I think a good place to start asking questions is with how to run workflow_execute.py and ask what each of the parameters are and where to get the information from them

Arguments *API key – got this and understand *url – got this and understand *workflow_id – I have created workflows and have been able to find what looks to be a workflow_id by clicking on the workflow name and selecting “Download or Export”. It seems this may be correct, is it? *history – a named history to use? Should this already exist? I have no idea here. *step=src=dataset_id - ??? I have no idea ??? I have seen how to create data libraries manually at the command line; does this factor in?

If anyone has information they can help me out with, it would be much appreciated.

Thanks

Craig Blackhart Computer Scientist Applied Engineering Technologies Los Alamos National Laboratory 505-665-6588 This message contains no information that requires ADC review

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