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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 has been made available. Specifically:
  • The CLC Genomics Cloud infrastructure, which is established using a CloudFormation template script, as described in Setting up and monitoring a CLC Genomics Cloud. Administrative privileges are required in the AWS account being used to set up this infrastructure.

  • At least one IAM user with appropriate permissions for submitting jobs to the CLC Genomics Cloud. The CloudFormation template script, described in Setting up and monitoring a CLC Genomics Cloud, includes the creation of one such user. Additional information about IAM users is also provided in that section.

  • At least one AWS S3 bucket for storing input data and results of analyses. These S3 buckets are not created by the scripts provided by QIAGEN. IAM users that will be submitting jobs to the CLC Genomics Cloud setup must have access to these buckets.

• A licensed CLC Workbench, with the CLC Cloud Module installed and licensed is required to submit jobs to the cloud for analysis.

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

  Note: Files in AWS S3 buckets can be browsed and downloaded, and data can be uploaded to AWS S3, without the CLC Cloud Module. See Working with AWS S3 using the Remote Files tab.

• 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/.

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