Latest improvements for QIAGEN CLC Genomics Cloud Engine

This update includes CLC Genomics Server 22.0.2, 22.0.1 and 22.0.

Upgrading from a CLC Genomics Cloud Engine 22.0.1, 22.0.0 or 21.x can be done by following the “Stack upgrade” process described in the GCE Administration manual.

For existing GCE 21.x setups in ap-northeast-1 (Tokyo) and us-west-1 (California): Just before running the create_stack.py script in the upgrade process, check that the availability zones in the DB_AZ1 and DB_AZ2 fields in the config/setup.sh file in the GCE administration host root account are available in your region. If they are not, then edit the values in those fields. E.g. for the Tokyo region, DB_AZ1=a and DB_AZ2=c would be acceptable.

CLC Genomics Cloud Engine 22.0.2 release page

Improvements

• The “update/update_jobmanager.py script in the GCE administration host now updates Apache Tomcat as well as the Apache HTTP Server. (See the “Applying security updates to the Job Manager” section in the GCE administration manual for details.)
• Various minor improvements

Compatibility

Workflow compatibility

Workflows to be run on the CLC Genomics Cloud Engine 22.0.2 are designed using a CLC Workbench. The recommended versions when working with CLC Genomics Cloud Engine 22.0.2 are:

• CLC Genomics Workbench 22.0.2
• CLC Main Workbench 22.0.2

Service/Client compatibility

Workflows can be submitted for execution using a compatible Workbench with the Cloud Plugin installed, and also via compatible versions of the CLC Genomics Server with the Cloud Server Plugin installed. The versions of Workbenches and CLC Servers compatible with CLC Genomics Cloud Engine 22.0.2 are 22.0, 22.0.1 and 22.0.2. 

Workflows can also be submitted for execution using  the CLC Genomics Cloud Engine Command Line Tools. The corresponding version is 22.0.2, but version 22.0.0 and 22.0.1 are also compatible. Workflow installer files that are submitted must be made with a CLC Workbench compatible with CLC Genomics Cloud Engine 22.0.2.

CLC Genomics Cloud Engine Command Line Tools 22.0.2

This is a compatibility release, as the corresponding client for the CLC Genomics Cloud Engine 22.0.2.

This update includes CLC Genomics Server 22.0.1 and 22.0.0.

Upgrading from a CLC Genomics Cloud Engine 22.0.0 or 21.x can be done by following the “Stack upgrade” process described in the GCE Administration manual.

For existing GCE 21.x setups in ap-northeast-1 (Tokyo) and us-west-1 (California): Just before running the create_stack.py script in the upgrade process, check that the availability zones in the DB_AZ1 and DB_AZ2 fields in the config/setup.sh file in the GCE administration host root account are available in your region. If they are not, then edit the values in those fields. E.g. for the Tokyo region, DB_AZ1=a and DB_AZ2=c would be acceptable.

Note: CLC Genomics Cloud Engine 22.0.0 can no longer be deployed due to configuration changes at AWS.

CLC Genomics Cloud Engine 22.0.1 release page

Improvements

• Apache security updates can now be manually applied using the GCE administration host. (See the “Applying security updates to the Job Manager” section in the GCE administration manual for details.)
• The installation chapter of the GCE administration manual has been rewritten. Other chapters have been revised.

Compatibility

Workflow compatibility

Workflows to be run on the CLC Genomics Cloud Engine 22.0.1 are designed using a CLC Workbench. The recommended versions when working with CLC Genomics Cloud Engine 22.0.1 are:

• CLC Genomics Workbench 22.0.1
• CLC Main Workbench 22.0.1

Service/Client compatibility

Workflows can be submitted for execution using a compatible Workbench with the Cloud Plugin installed, and also via compatible versions of the CLC Genomics Server with the Cloud Server Plugin installed. The versions of Workbenches and CLC Servers compatible with CLC Genomics Cloud Engine 22.0.1 are 22.0 and 22.0.1. 

Workflows can also be submitted for execution using  the CLC Genomics Cloud Engine Command Line Tools. The corresponding version is 22.0.1, but version 22.0.0 is also compatible. Workflow installer files that are submitted must be made with a CLC Workbench compatible with CLC Genomics Cloud Engine 22.0.1.

CLC Genomics Cloud Engine Command Line Tools 22.0.1

This is a compatibility release, as the corresponding client for the CLC Genomics Cloud Engine 22.0.1.

CLC Genomics Cloud Engine 21.x environments can be updated to 22.0.0 by following the “Stack upgrade” process described in the GCE Administration manual.

Improvements

• Deployment has been simplified by the inclusion of a new script, create_user_pool.py that, in a single step, deploys an AWS Cognito user pool and configures GCE to use it.
• During deployment via CloudFormation access to the Administration Host and Job Manager can be limited to a fixed IP address or address range, thereby increasing the security of the setup.
• Restrictions relating to the use of input modifying tools in workflows executed on GCE have been removed. See the CLC Genomics Workbench 22.0 latest improvement notes for more on changes to the use of such tools in a workflow context.
• Various minor improvements

Changes

Amazon Linux 2 is now used in the AWS Beanstalk apps.

Compatibility

Workflow compatibility

Workflows to be run on the CLC Genomics Cloud Engine 22.0.0 are designed using a CLC Workbench compatible with the CLC Genomics Server run by GCE. For this release, these are:

• CLC Genomics Workbench 22.0
• CLC Main Workbench 22.0

Service/Client compatibility

CLC Genomics Cloud Engine 22.0.0 contains CLC Genomics Server 22.0. Workflows can be submitted to run on CLC Genomics Cloud Engine 22.0.0 from compatible versions of CLC Workbenches with the Cloud Plugin installed and configured, and from compatible versions of CLC Genomics Server with the Cloud Server Plugin installed and configured.

The CLC Genomics Cloud Engine Command Line Tools 22.0.0 is the corresponding command line client for the CLC Genomics Cloud Engine 22.0.0.

CLC Genomics Cloud Engine Command Line Tools 22.0.0

This is the corresponding client for the CLC Genomics Cloud Engine 22.0.0.

Improvements

• When required workflow parameters are not provided when submitting to GCE, this is now reported directly. Previously, this information was reported only in the gce.log file placed in the output location on S3.

Bugfixes

Various minor bugfixes