Story #8654

Updated by Peter Amstutz about 7 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.