Integrating third party tools into CLC software
Third party applications and scripts can be integrated with CLC software as "external applications".
When included in a workflow, external applications on a CLC Server can be submitted for execution on the CLC Server or in the cloud using a CLC Workbench or using the CLC Server Command Line Tools.
Workflows containing external applications can also be submitted for execution on the cloud directly from a CLC Workbench, without connecting to a CLC Server. This requires the external applications to be installed on the CLC Workbench and then added to the workflow. Such workflows can only be executed on the cloud.
Related documentation links
- Creating and configuring external applications, done in the web client of the CLC Server: 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 to others. See "Web admin access" on https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Controlling_access_server_server_tasks_external_data.html.
- Adding an external application to a workflow, done in the Workflow Editor of a CLC Workbench: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=External_applications_in_workflows.html.
Links to general information about creating and editing workflows are provided at the bottom of that page.
- Submitting workflows to the cloud from a CLC Workbench via a CLC Server: 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: Submitting workflows to the cloud using the CLC Server Command Line Tools
- Installing external applications on a CLC Workbench: Installing external applications in a CLC Workbench
- Submitting workflows to the cloud from a CLC Workbench directly: Submitting analyses to AWS from a Workbench
Extra requirements for external applications to be run on the cloud
- To run an external application on the cloud, the resources referred to by it must be available 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.
- When launching via a CLC Server, the external application is present on the CLC Server and accessible to the user launching the workflow.
- When launching directly from a CLC Workbench, the external application has been installed on the CLC Workbench and then included in the workflow (see Installing external applications in a CLC Workbench).
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