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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 to the cloud via a CLC Server using a CLC Workbench
  • Submitting workflows to the cloud using the CLC Server Command Line Tools
• Integrating third party tools into CLC software
  • Installing external applications in a CLC Workbench
• 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, AMIs and images
  • System file retention policies
  • Making custom plugins available for cloud analyses

General information about outputs from cloud analyses

All results generated on the cloud are stored on the cloud. To view results in a CLC Workbench, the data must be downloaded to a local CLC location. This is easily done via a CLC Workbench via the Remote Files tab, described in Working with AWS S3 using the Remote Files tab, and via the Processes tab, described in Accessing results from the Processes tab.

AWS charges for downloading data. In CLC Workbenches, when the download size exceeds 1 GB, you are prompted for confirmation that you wish to proceed. The size required to trigger this warning can be changed in the General section of the Workbench Preferences (figure 6.4). When downloading via the CLC Server web interface, a window pops up listing the selected files and providing the total download size. After selecting whether to download to a CLC location or to a CLC Server import/export area, you are prompted to selected a specific location to download to. For details, see https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Browse_AWS_S3_locations.html.

Figure 6.5: Download cost warning dialogs are shown whenever the size of a download from AWS S3 exceeds the value configured in the Workbench Preferences. By default, the value is set to 1000 MB.

For downloading large amounts of data, we recommend using dedicated software for interacting with AWS S3. CLC data downloaded using external software can be imported into the CLC Workbench using Standard Import, described at https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Standard_import.html.

Download all contained tracks when downloading track lists to view

Track lists are small elements that refer to tracks. When downloading track lists to view, the track list and all the tracks contained must be downloaded at the same time.

If this is not done, one or more of the tracks in the track list will not be resolved. The relevant links between track lists and the tracks referred to cannot be made if these elements are downloaded separately.

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