Cloud connections via a CLC Server
With the Cloud Server Plugin installed on the CLC Genomics Server, you can submit workflows to run on a CLC Genomics Cloud Engine (GCE) via the CLC Genomics Server. The Cloud Job Search tool can then be used to find jobs and download results from these analyses.
Choosing to launch analyses that make use of remote data via the CLC Server can be particularly useful when working with large amounts of data, as it will then not be downloaded to your local system.
in addition, working with a CLC Server means the CLC Workbench does not need to be left running once the job has been submitted.
Note:
- There are no user permissions on jobs in GCE. This means that GCE users will be able to find each other's jobs, for example by using the Cloud Job Search functionality in their Workbench.
- It is possible to prevent a CLC Workbench user from being able to submit jobs to GCE by configuring permissions for each cloud preset. GCE presets are described in Configuring GCE presets
Information about installing server plugins is at https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Server_plugins.html.
Importing data from Illumina Basespace via a CLC Server
When launching analyses to run on a CLC Server or to run on GCE via the CLC Server, you can select data from Illumina Basespace as input. For this, you need an Illumina BaseSpace account, but no configuration of the CLC Server or the Cloud Server Plugin is necessary.
Importing data from and exporting data to Amazon S3 via a CLC Server
When launching analyses to run on a CLC Server or to run on GCE via the CLC Server, you can select data from an active Amazon S3 location that has been configured in the CLC Server. Documentation about configuring Amazon S3 locations is provided in the CLC Server manual, available from https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/User_Manual.pdf
Launching jobs to run on a CLC Genomics Cloud Engine via a CLC Server
To submit a workflow to run on GCE via the CLC Genomics Server, choose the option "CLC Genomics Cloud Engine (via CLC Server)" in the launch wizard for the workflow. A drop-down menu in the launch wizard allows you to select the GCE preset to use for that job. A GCE preset specifies the type of machine a job should be run on, and some other details about how the job should be handled.
The option to submit jobs via a CLC Server is available when the Workbench is connected to a CLC Genomics Server with the Cloud Server Plugin installed and configured, and where one or more GCE presets is available. See Configuring the Cloud Server Plugin.
When submitting jobs to the cloud through the CLC Genomics Server, the user account registered is the user logged into the CLC Server. No configuration of the CLC Workbench is needed for this. When submitting via the CLC Server, the AWS and GCE settings are obtained from the CLC Server.
Finding jobs and results submitted via the CLC Server using Cloud Job Search
The Cloud Job Search tool in a CLC Workbench with the Cloud Plugin installed can be used to find jobs and download results from analyses submitted to CLC Genomics Cloud Engine via a CLC Server. To find these jobs, the AWS locations, and the 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.
The Cloud Job Search tool is described further in Cloud Job Search.
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