Deleting or redeploying CLC Genomics Cloud infrastructure on AWS
Deleting individual AWS Batch queues
To delete the cgc-small, cgc-medium or cgc-large AWS Batch queue, created when the CLC Genomics Cloud infrastructure was set up, go to AWS Batch | Job queues, select the relevant queue and select the "Disable" option under the Actions menu. Once it is disabled, select the queue again, and select the "Delete" option under the Actions menu.
To delete an AWS Batch queue added after the initial deployment of the CLC Genomics Cloud infrastructure, go to CloudFormation | Stacks, select the relevant stack and click the Delete stack button.
Deleting CLC Genomics Cloud infrastructure
The steps for deleting a standard CGC environment in the AWS Console are:
- Empty the contents of the cgc-system bucket.
In S3 | General purpose buckets, select the cgc-system bucket and click the Empty button. - Delete old job definitions.
To delete job definitions, which are created if jobs have been run using the CGC infrastructure, go to AWS Batch | Job definitions, select each job definitions with a name that start with cwe and select "Deregister" under the Actions menu. - Delete the stacks of any additional job queues created.
If additional queues were created using the template described in Adding more AWS Batch queues for CLC jobs, then in CloudFormation | Stacks, select each of these in turn and click the Delete stack button.At this point, there should be five stacks associated with the CLC Genomics Cloud infrastructure listed in CloudFormation | Stacks: the main stack and four nested stacks.
- Delete the main stack.
In CloudFormation | Stacks, select the main stack, and click the Delete stack button.All five stacks should be deleted by taking this action. This may take some time.
Note: If the SubmitterUser or BrowserUser policy has been used as the basis of permissions for other IAM users, the initial attempt to delete the main stack may fail. In this case, try to delete the stack again this time choosing the option Force delete this entire stack. This option causes resources that could not be deleted to be retained, with their dependencies intact, while deleting the rest of the stack.
Redeploying CLC Genomics Cloud infrastructure
To redeploy CGC infrastructure on AWS:
- Delete the existing CGC resources, as described above.
- Deploy new CGC resources, as described in Setting up AWS resources.
- Optionally, add more queues, as described in Adding more AWS Batch queues for CLC jobs.
Note that:
- If queue names have been changed relative to an earlier setup, cloud presets on CLC Servers may need to be updated.
- If credentials for the SubmitterUser or BrowserUser from an earlier setup have been used in AWS Connections, the login details will need to be updated.
- If the SubmitterUser or BrowserUser permission policy has been used as the basis of permissions for other IAM users, those users will need to have the new SubmitterUser or BrowserUser's permissions policy added.