Using the Cloud Server Plugin with the CLC Genomics Server

When connected to a CLC Genomics Server where the Cloud Server Plugin has been installed and configured by the server administrator, it is possible to import data to and export data from AWS S3 and submit jobs to the CLC Genomics Cloud Engine through the CLC Genomics Server. This can be particularly useful when a large amount of data is located in a server location or a file system location available to the server. In these cases, the data will be uploaded to the cloud directly from the CLC Genomics Server, thereby removing the need to keep the CLC Workbench running during the upload.

Submitting jobs to the cloud through the CLC Genomics Server works in a very similar way to submitting directly from a CLC Workbench. In the first wizard step when running the workflow, select "CLC Server Cloud". The drop-down menu contains the cloud presets that have been configured by the server administrator. A cloud preset controls characteristics for a job submission, such as hardware requirements and whether the results should be automatically downloaded or not. The server administrator also controls the cache bucket that will be used for submitting jobs through the CLC Genomics Server.

When submitting jobs to the cloud through the CLC Genomics Server, the user account registered for the submission will be the user logged into the CLC Genomics Server. It is not the user from the GCE configuration settings in the cloud configuration dialog in the CLC Workbench. In practice, these user accounts may the same.

When a CLC Workbench is connected to a cloud-enabled CLC Genomics Server and no configuration details have been entered in the CLC Workbench itself, then the CLC Workbench will automatically obtain the AWS and GCE settings from the CLC Genomics Server.

Finding jobs and results submitted via the CLC Server using Cloud Job Search

To use the Cloud Job Search tool to find jobs and results of jobs submitted to CLC Genomics Cloud Engine via a CLC Genomics Server, the AWS and GCE settings specified in the CLC Workbench cloud configuration dialog should either be empty, in which case the details of the configuration settings for the Cloud Server Plugin will be used, or must match those specified in the Cloud Server Plugin configuration in the CLC Genomics Server.

The "Only from logged-in user" option in the Cloud Job Search tool will find jobs submitted by both the user authenticated through the cloud configuration dialog and the user logged into the CLC Genomics Server. This is most noticeable if these user names differ.