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RyuGoo-Saba

RyuGoo-Saba is an execution engine aimed at running Common Workflow Language (CWL) on cloud computing. The differences from the other cloud enabled CWL runners like Toil and Cromwell is aimed at building a cluster environment including the launch of VM just by user inputting user information of each cloud vendor.

In the present situation, it correspond only to Azure, Alpha version.

Visit GitHub wiki for more details.

Prerequisites

  • docker
  • docker-compose (version 3)

Install

Use git to fetch the source from GitHub and use docker-compose to create the CLI environment:

$ git clone https://github.com/Rhelixa-inc/RyuGoo-Saba.git
$ docker-compose -f ./RyuGoo-Saba/SabaCLI/docker-compose.CLI.yml up -d --build
$ docker-compose -f ./RyuGoo-Saba/SabaCLI/docker-compose.CLI.yml exec cli bash
$ saba

This will do to Create a Docker environment that includes

  • SabaCLI
  • Ansible
  • Azure CLI

The reason to launch the CLI as a Docker-compose environment is to separate the ssh connection information and Azure credential information from those inside the user's PC.

Construct cluster environment and execute job

$ saba start -u [azure-user-id] -p [azure-user-password] -s [azure-subscription-id]
$ saba job submit -s [input-data-urls] -c [cwl-file-urls] -i [instance-size] -d [disk-size]
  • Launch a VM and do docker-compose up as SabaMaster, which will be a job handler.
  • Using SabaMaster's REST API endpoint, start another VM and do docker-compose up as SabaWorker, which will be a job executer.
  • For each job, it is executed in one VM, and when finished job, upload results and log to object storage and delete VM.