Story #8654

Updated by Peter Amstutz over 3 years ago

We want to do this to make it as easy as possible to run CWL workflows in Arvados. Adding it to arvados/jobs makes that simple because we already have infrastructure to keep it up-to-date on clusters.

* Update the arvados/jobs image to be based on Debian jessie.
* Add the cwl-runner package to arvados/jobs.
* Add a cwl-runner crunch_script to the Arvados repository to call arvados_cwl by filling in inputs from the current job's script_parameters.
* Add @arvados-cwl-runner --submit@ option that submits a job that runs cwl-runner

Acceptance criteria:
- User can use @arvados-cwl-runner --submit tool.cwl input.json@ to submit a CWL job, including uploading any workflow and input dependencies that are not already present on the target Arvados instance. This will create a job to execute the CWL workflow and submits additional jobs that do the actual work so that the workflow can run unattended similarly to existing Arvados pipelines.

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