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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

CLC Genomics Cloud requirements

The requirements for a fully functional CLC Genomics Cloud setup are:

• Access to an AWS account where the relevant infrastructure is available.

  Establishing the necessary infrastructure on AWS is described in Setting up and monitoring a CLC Genomics Cloud. It requires administrative privileges in the AWS account being used.

• A licensed CLC Workbench, with the CLC Cloud Module installed and licensed.

  Installation of the CLC Cloud Module is described in Installing Workbench modules.

  If the CLC Cloud Module is installed but not licensed, or you are working with a Workbench in Viewing Mode, you can interact with files on AWS S3, but analyses cannot be submitted to run on AWS.

• If analyses will be submitted via a CLC Server, the Cloud Server Plugin must be installed and cloud presets configured.

  Working with the CLC Server is described in Using a CLC Server to interact with a CLC Genomics Cloud.

General system requirements for CLC software are provided on https://digitalinsights.qiagen.com/technical-support/system-requirements/

Viewing Mode is described at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Viewing_mode.html.

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