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Story #8654

closed

[CWL] Incorporate cwl-runner into arvados/jobs

Added by Brett Smith almost 7 years ago. Updated almost 7 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
Crunch
Target version:
Start date:
03/07/2016
Due date:
% Done:

100%

Estimated time:
(Total: 0.00 h)
Story points:
1.0

Description

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.


Subtasks 3 (0 open3 closed)

Task #8777: Pass CWL conformance tests with --submitResolvedPeter Amstutz03/07/2016

Actions
Task #8735: Add cwl-runner --submitResolvedPeter Amstutz03/07/2016

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Task #8736: ReviewResolvedRadhika Chippada03/07/2016

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Related issues

Related to Arvados - Story #8815: [Crunch] crunch-job bind mounts crunchrunner & host certs file at well known location inside containerResolvedPeter Amstutz03/29/2016

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