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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 using the CLC Server Command Line Tools
• Integrating third party tools into CLC software
• 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 and AMIs
  • System file retention policies
  • Making custom plugins available for cloud analyses

Integrating third party tools into CLC software

Third party applications can be integrated with CLC software by configuring them as external applications using a CLC Server. Workflows containing external applications can be submitted for execution on the cloud, like any other workflow.

Configuring external applications and including them in workflows is described in the External Applications chapter of the CLC Server administration manual: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=External_applications.html

By default, only administrative users can configure external applications, but permissions can be granted more broadly, as described under "Web admin access" on https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Controlling_access_server_server_tasks_external_data.html

Resources referred to in an external application must be available when it is run on the cloud. For containerized external applications that can be successfully run on a CLC Server, this requirement will generally be met. For standard external applications, the tools referred to in the configuration, including any referred to in an included script in that configuration, need to be available in the Linux image used when the job is run on AWS. See AWS Batch queues, compute environments and AMIs for information about the compute resources in a CLC Genomics Cloud setup.

Note: When running a workflow containing external applications available on a CLC Server, there must be a connection to that CLC Server when launching the workflow. This can mean using a CLC Workbench connected to the CLC Server, or submitting workflows installed on the CLC Server using the CLC Server Command Line Tools.

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