Overview

This section describes how to run Toil in various environments, including locally, in the cloud, and with using CWL.

Specifically, the running Toil section documents detail for the following:

• Toil Workflow Options and Command Line Interface
  • Logging
  • Stats
  • Restart
  • Clean
  • Batch system
  • Default cores, disk, and memory
  • Job store
  • Miscellaneous
  • Running Workflows with Services
• CWL in Toil
  • Running CWL Locally
  • Running CWL in the Cloud
• Deploying a Workflow
  • Deploying a Local Workflow
  • Deploying a Remote Workflow
    • Remote deployment with sibling modules
    • Remotely deploying a package hierarchy
    • Relying on shared filesystems
  • Using Docker with Toil
• Running in AWS
  • Toil Provisioner
  • Details about Launching a Cluster in AWS
    • Static Provisioning
    • Uploading Workflows
    • Running a Workflow with Autoscaling
    • Preemptability
  • Cluster Utilities
    • launch-cluster
    • ssh-cluster
    • rsync-cluster
    • destroy-cluster
• Running in Azure
  • Launch a leader node in Azure
  • Launch a Toil Mesos Cluster
• Running in Openstack
• Running in GCE
• Running in HPC Environments