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• Introduction to the CLC Genomics Cloud
  • Overview of CLC Genomics Cloud
  • CLC Genomics Cloud requirements
  • Contact information
  • Installing the CLC Cloud Module
    • Licensing modules
    • Uninstalling modules
  • Installing the Cloud Server Plugin
• Setting up CLC Genomics Cloud resources on AWS
  • Setting up AWS resources
  • Adding more AWS Batch queues for CLC jobs
  • Adding more AWS IAM users
  • Deleting or redeploying CLC Genomics Cloud infrastructure on AWS
• Using a CLC Workbench to work on the cloud
  • Prerequisites for working on the cloud using a Workbench
  • Configuring an AWS Connection in the Workbench
  • Submitting analyses to AWS from a Workbench
  • Working with AWS S3 using the Remote Files tab
  • Accessing results from the Processes tab
• Using a CLC Server to work on the cloud
  • Benefits of submitting jobs via a CLC Server
  • AWS Connections in the CLC Server
  • Configuring cloud presets
  • Browse AWS S3 locations
  • Submitting workflows to the cloud via a CLC Server using a CLC Workbench
  • Submitting workflows to the cloud using the CLC Server Command Line Tools
• Integrating third party tools into CLC software
  • Installing external applications in a CLC Workbench
• General information about inputs and results
  • General information about input data for cloud analyses
    • Reference data for analyses on the cloud
    • Using locally held data for analyses on AWS S3
  • General information about outputs from cloud analyses
• Monitoring and reviewing CLC cloud jobs
  • Using a CLC Workbench to monitor and review cloud jobs
  • Using a CLC Server to monitor and review cloud jobs
  • Using the AWS Console to monitor and review cloud jobs
• Appendix
  • Standard AWS Batch queues for CLC Genomics Cloud
  • AWS Batch queues, compute environments, AMIs and images
  • System file retention policies
  • Making custom plugins available for cloud analyses

Prerequisites for working on the cloud using a Workbench

Submitting analyses to run on AWS

To submit jobs to run on AWS from a CLC Workbench you need:

• A licensed CLC Workbench.
• The CLC Cloud Module installed on the Workbench and licensed (see Installation of modules).
• An AWS Connection configured with AWS IAM user credentials for a user with permission to submit analyses to run on AWS (see Configuring the AWS Connection in the Workbench).

An option called CLC Genomics Cloud is enabled in launch wizards when the setup is ready (see Running analyses on AWS).

Working with AWS S3 only

If you only wish to browse and access data stored on AWS S3 from your CLC Workbench you need:

• A CLC Workbench with the CLC Cloud Module installed. Licenses for the Workbench and module are not required (see Installation of modules).
• An AWS Connection configured with AWS IAM user credentials with appropriate permissions to work with AWS S3 buckets in your account. These could be the same user credentials used for submitting jobs to run on AWS, or an IAM user with permissions limited to working with files on AWS S3 (see Configuring the AWS Connection in the Workbench).

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