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Execution Environments

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fnothaft

Talk from GA4GH meeting at ASHG/San Diego meeting about support for efficiently executing code on top of the GA4GH APIs.

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Execution Environments Frank Austin Nothaft
v0.5 API Support data access to reads/variants over REST Most existing applications using API are interactive
Batch Processing Is REST the correct approach? API is consistent for both local & remote data But, has overhead (perf + admin) for local data Approaches moving forward: Shims to current file formats Native interface to Hadoop ecosystem?
Common Workflow Language Pain point: how do we build reproducible pipelines of tasks? A group has started building a common workflow description language for bioinformatics: https://groups.google.com/forum/#!forum/ common-workflow-language Should the GA4GH take this task on?

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Execution Environments

  • 2. v0.5 API Support data access to reads/variants over REST Most existing applications using API are interactive
  • 3. Batch Processing Is REST the correct approach? API is consistent for both local & remote data But, has overhead (perf + admin) for local data Approaches moving forward: Shims to current file formats Native interface to Hadoop ecosystem?
  • 4. Common Workflow Language Pain point: how do we build reproducible pipelines of tasks? A group has started building a common workflow description language for bioinformatics: https://groups.google.com/forum/#!forum/ common-workflow-language Should the GA4GH take this task on?