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Events/GCC2011/Workflows and API


  • Kanwei Li
  • Dannon Baker
  • 15 participants

General discussion: Execution model of workflows so that we can use it through the API.

How do you get a key?

  • User -> API Keys after you register

When you delete a user, API key needs to be deleted/disabled.

Should better publicize the common.py script that provides helper Python functions. Create a project in Tool Shed to add wrappers for different languages

Bigger picture

  • Integration with other systems
  • How far has a workflow progressed? A histories API could show the status of the workflow execution

What do we want to expose?

  • Eventually anything that can be interactive in Galaxy.

Use case:

  • External links in data libraries when files are moved, want to modify the new location through the API to facilitate data migration
  • Getting access to physical files through the API.

Definition of workflow API access for inputs

  • Show details for workflow API call needs to return a dict of { NAME: TYPE }
  • Then you can call the create workflow call with dict of { NAME: INPUT }
  • Right now you can ONLY enter HDA or LDDA inputs. Other datatypes needs to be implemented

Running workflows by the web thread versus by a separate daemon. Problems: accidentally running multiple workflows etc, as a single user since Galaxy has one user

Longer-term Wishlist:

  • Conditionals in workflows
  • Running single tool in API
  • Getting an API key from LDAP / external auth, not hardcoding API key