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• Introduction
  • Prerequisites
• Configuring cloud-based data locations
  • Configuring AWS credentials
  • Configuring Illumina BaseSpace credentials
• Configuring the cloud connection
• Importing data from the cloud
• Exporting data to the cloud
• Running workflows in the cloud
• Cloud Job Search
  • Downloading all results
  • Selective download of results
• Using the Cloud Server Plugin with the CLC Genomics Server
  • Configuring the Cloud Server Plugin
    • Configuring the AWS and CLC Genomics Cloud Engine settings
  • Configuring cloud presets
• External applications in the cloud
• Troubleshooting
• Installing and uninstalling Workbench plugins
  • Installation of Workbench plugins
  • Uninstalling Workbench plugins

External applications in the cloud

Third party applications can be integrated into the CLC environment by configuring them as external applications. Containerized external applications can be used in workflows to be executed on the CLC Genomics Cloud Engine if the container is in the Amazon Elastic Container Repository (ECR) on the same Amazon account where the CLC Genomics Cloud Engine is deployed.

Information about configuring external applications, and exporting the configurations for use by the CLC Genomics Cloud Engine can be found in the External applications chapter of the CLC Genomics Server manual at https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual==External_applications.html

Creating and configuring workflows with external applications

Creating and editing workflows is done in the CLC Workbench, as described at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Workflows.html.

Workflow elements will be available for:

• External applications available on a CLC Genomics Server, if the Workbench is connected to one.
• External applications described in the configuration file located on S3, where that location has been entered into the Workbench Preferences, under the Advanced tab, and the relevant AWS credentials have been configured, so you have access to the S3 bucket (see Configuring the cloud connection).

External applications configurations are exported to S3 from a CLC Genomics Server by an administrative user, as described at https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual==Import_export_external_application_configurations.html

Please ask your CLC Genomics Server administrator for the s3 URL to configure in the CLC Workbench Preferences. This is usually of particular relevance if you wish to submit workflows containing external applications to the CLC Genomics Cloud Engine without connecting to a CLC Genomics Server.

Submitting workflows with external applications to run on GCE

Workflows can be submitted for analysis on the CLC Genomics Cloud Engine by a CLC Workbench, with or without a connection to a CLC Genomics Server, or using the CLC Server Command Line Tools.

Submitting via a CLC Workbench without a connection to a CLC Server

The location of the exported external application configuration file in S3 must be configured in the Workbench Preferences. All the external applications included in the workflow must be described in the configuration file in S3.

Subitting via a CLC Workbench with a connection to a CLC Server

The location of the exported external application configuration file in S3 is only needed if there are external applications in the workflow that are not present on the server, (but which are described in the configuration file on S3).

Submitting via a CLC Server using the CLC Server Command Line Tools or a CLC Workbench

The external applications included in the workflow must be configured on the CLC Server.

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