Latest improvements for CLC Genomics Cloud Engine


CLC Genomics Cloud Engine 1.3.9

Release date: 2019-03-06

CLC Genomics Cloud Engine 1.3.9

This update contains changes to the infrastructure as well as the software. Because of the infrastructure changes it is necessary to redeploy the CLC Genomics Cloud Engine.

Improvements

  • Release now includes CLC Genomics Server version 9.0, 10.0.1 and 11.0 and the system administrator can change which of the versions to use.
  • Service to service integration is now possible through a convenient REST API. A Swagger Specification is provided with the REST API, which can be used to generate client code for easier integration.
  • Improved auto scaling, which scales faster to a large amount of servers and shuts them down faster as well.
  • AWS resources used by CLC Genomics Cloud Engine can now be tagged. The tags are defined during deployment of CLC Genomics Cloud Engine.
  • Improved error messages when a job fails because of file corruption.
  • Encryption key moved to database CloudFormation stack. As a result there is no need for re-enrolling users after a redeployment of the other GCE stacks.

Bugfixes

  • Job definition files from cancelled job are now deleted when the job is cancelled.
  • Unused AWS SQS queues are now deleted.
  • "get parameter" jobs are now displayed as successfully completed in the CLC Genomics Cloud Engine web interface.
Frequently Asked Questions

CLC Genomics Cloud Engine Command Line Tools 1.3.9

Bugfixes

  • Changing instance type using the Command Line Tools is now memory efficient. Previously it would sometimes cause an out of memory error on low memory systems.

Compatibility

The CLC Genomics Cloud Engine Command Line Tools 1.3.9 is the corresponding client for the CLC Genomics Cloud Engine 1.3.9. We always recommend running the corresponding versions of service and client and for this release in particular it is not possible to access the CLC Genomics Cloud Engine 1.3.9 with an earlier version of the CLC Genomics Cloud Engine Command Line Tools. Nor is it possible to access an earlier version of the CLC Genomics Cloud Engine with the CLC Genomics Cloud Engine Command Line Tools 1.3.9. The CLC Genomics Cloud Engine can be run using the CLC Genomics Server 11.0, 10.0.1 or 9.0. Workflows to be run on the CLC Genomics Cloud Engine 1.3.9 are designed using a CLC Workbench. Workflow installer files should be made using a CLC Workbench compatible with the CLC Genomics Server used for GCE. Recommended versions for this purpose are listed below. The CLC Workbench versions that correspond to a given CLC Genomics Server version are shown in bold font. These are preferred for making workflow installers to be run on GCE. CLC Genomics Server 11.0
  • CLC Genomics Workbench 12.0
  • CLC Main Workbench 8.1
CLC Genomics Server 10.0.1
  • CLC Genomics Workbench 11.0, 11.0.1
  • Biomedical Genomics Workbench 5.0, 5.0.1
  • CLC Main Workbench 8.0. 8.0.1
CLC Genomics Server 9.0
  • CLC Genomics Workbench 10.0
  • Biomedical Genomics Workbench 4.0
  • CLC Main Workbench 7.8


CLC Genomics Cloud Engine 1.2.4

Release date: 2018-10-01

CLC Genomics Cloud Engine 1.2.4

This update contains only changes to deployment of the infrastructure configuration.

Bugfixes

  • Fixed a deployment issue caused by AWS API changes.

Frequently Asked Questions

CLC Genomics Cloud Engine Command Line Tools 1.2.4

Nothing has changed.

Compatibility

The CLC Genomics Cloud Engine Command Line Tools 1.2.4 is the corresponding client for the CLC Genomics Cloud Engine 1.2.4.

We recommend running the corresponding versions of service and client. However, CLC Genomics Cloud Engine Command Line Tools 1.2.4 can be used with CLC Genomics Cloud Engine 1.2.2, 1.1.1, 1.0.15, 1.0.6 and 1.0.4 and CLC Genomics Cloud Engine Command Line Tools 1.2.2, 1.1.1, 1.0.15, 1.0.6 and 1.0.4 can be used with CLC Genomics Cloud Engine 1.2.4.

CLC Genomics Cloud Engine includes CLC Genomics Server 10.0.1.

Workflows to be run on the CLC Genomics Cloud Engine 1.2.4 can be designed using Workbenches compatible with CLC Genomics Server 10.0.1. These are:

  • CLC Genomics Workbench 11.0.1 and CLC Genomics Workbench 11.0
  • Biomedical Genomics Workbench 5.0.1 and Biomedical Genomics Workbench 5.0


CLC Genomics Cloud Engine 1.2.2

Release date: 2018-07-05

CLC Genomics Cloud Engine 1.2.2

This update contains only changes to the software. There are no changes to the infrastructure configuration.

Bugfixes

  • Fixed a bug that caused an out of memory error when changing the Job Executor instance type using the admin host.

Improvements

  • Each AWS resource created during deployment can now be tagged.
  • AWS Cognito can be used as the identity provider.
  • The CLC Genomics Server included in GCE has been upgraded to version 10.0.1.
  • When self-signed certificates are generated they will now be valid for 30 years rather than 1 year.
  • The supported AWS regions have been expanded to the following: N. Virginia, Ohio, N. California, Oregon, Frankfurt, Ireland, Tokyo, Seoul, Sydney and Mumbai.

Frequently Asked Questions

CLC Genomics Cloud Engine Command Line Tools 1.2.2

Improvements

  • The stability of the "job parameters" command has been improved.

Compatibility

The CLC Genomics Cloud Engine Command Line Tools 1.2.2 is the corresponding client for the CLC Genomics Cloud Engine 1.2.2.

We recommend running the corresponding versions of service and client. However, CLC Genomics Cloud Engine Command Line Tools 1.2.2 can be used with CLC Genomics Cloud Engine 1.1.1, 1.0.15, 1.0.6 and 1.0.4, and CLC Genomics Cloud Engine Command Line Tools 1.1.1, 1.0.15, 1.0.6 and 1.0.4 can be used with CLC Genomics Cloud Engine 1.2.2.

The CLC Genomics Cloud Engine includes the CLC Genomics Server 10.0.1.

Workflows to be run on the CLC Genomics Cloud Engine 1.2.2 can be designed using Workbenches compatible with CLC Genomics Server 10.0.1. These are:

  • CLC Genomics Workbench 11.0.1 and CLC Genomics Workbench 11.0
  • Biomedical Genomics Workbench 5.0.1 and Biomedical Genomics Workbench 5.0


CLC Genomics Cloud Engine 1.1.1

Release date: 2017-11-07

This update contains only changes to the software. There are no changes to the infrastructure configuration.

Improvements

  • CLC Server plugins can now be installed in GCE. Previously only the preinstalled plugins could be used.
  • Changed name of "install host" to "administration host" in accordance with the fact that it is used after install for tasks like software updates and plugin deployment.

  • Added "download-settings" script to administration host that will allow the user to quickly get the configuration of an existing GCE stack or shift between configurations of different stacks.

  • It is now fully supported to analyse input data stored in other regions and on other accounts, than the region and account where the GCE service is installed.

Bugfixes

  • Fixed a bug which prevented the Workflow Executor from being updated during a software update. 

 

Frequently Asked Questions

CLC Genomics Cloud Engine Command Line Tools 1.1.1

Improvements

  • Improved stability of communication with the GCE service.

Bugfixes

  • Profiles created with the "gce config ... -profile <profile name>" command is now actually used in other CLT commands where the "-profile" parameter is used.

  • It is no longer required to have the AWS CLI installed for the GCE CLT to work.-

Compatibility

 The CLC Genomics Cloud Engine Command Line Tools 1.1.1 is the corresponding client for the CLC Genomics Cloud Engine 1.1.1.

We recommend running the corresponding versions of service and client. However, CLC Genomics Cloud Engine Command Line Tools 1.1.1 can be used with CLC Genomics Cloud Engine 1.0.4, 1.0.6 and 1.0.15, and CLC Genomics Cloud Engine Command Line Tools 1.0.4,1.0.6 and 10.0.15 can be used with CLC Genomics Cloud Engine 1.1.1.

The CLC Genomics Cloud Engine includes the CLC Genomics Server 9.0.

Workflows to be run on the CLC Genomics Cloud Engine 1.1.1 can be designed using Workbenches compatible with CLC Genomics Server 9.0. These are:

  • CLC Genomics Workbench 10.0.0 and 10.0.1
  • Biomedical Genomics Workbench 4.0

Information on getting Workbench installers



CLC Genomics Cloud Engine 1.0.15

Release date: 2017-08-25

CLC Genomics Cloud Engine 1.0.15

This update contains only changes to the software. There are no changes to the infrastructure configuration.

Bugfixes

  • Jobs will no longer fail during the final phases of performing the analysis because of AWS S3 occasionally failing to respond to requests. GCE now handles this with retries in accordance with the AWS recommended exponential backoff strategy.

Improvements

  • The new Administration Host replaces the Installation Host. The Administration Host is installed separately from the "preinstall" stack, via a separate CloudFormation script. To learn more read the "Install GCE on Amazon" section and the new "Upgrade an Existing GCE Solution" section of the Administration Manual.
  • Included with the Administration Host is a new script that will update GCE from a previous version to the newest version. To learn more read the new "Upgrade an Existing GCE Solution" section of the Administration Manual.

Frequently Asked Questions

CLC Genomics Cloud Engine Command Line Tools 1.0.15

Bugfixes

  • Job submits no longer fail because of AWS S3 occasionally failing to respond to requests. GCE CLT now handles this with retries in accordance with the AWS recommended exponential backoff strategy.

Compatibility

The CLC Genomics Cloud Engine Command Line Tools 1.0.15 is the corresponding client for the CLC Genomics Cloud Engine 1.0.15.

We recommend running the corresponding versions of service and client. However, CLC Genomics Cloud Engine Command Line Tools 1.0.15 can be  used with CLC Genomics Cloud Engine 1.0.4 and 1.0.6, and CLC Genomics Cloud Engine Command Line Tools 1.0.4 and 1.0.6 can be used with CLC Genomics Cloud Engine 1.0.15.

The CLC Genomics Cloud Engine includes the CLC Genomics Server 9.0.

Workflows to be run on the CLC Genomics Cloud Engine 1.0.15 can be designed using Workbenches compatible with CLC Genomics Server 10.0.0 and 10.0.1. These are:

  • CLC Genomics Workbench 10.0.0 and 10.0.1
  • Biomedical Genomics Workbench 4.0

Information on getting Workbench installers



CLC Genomics Cloud Engine 1.0.6

Release date: 2017-06-27

CLC Genomics Cloud Engine 1.0.6

Bug fixes

  • Fixed an issue where log URLs were not returned if a job failed early on.

CLC Genomics Cloud Engine Command Line Tools

Improvements

  • The option -profile has been added to several commands, to support the use of multiple GCE setups.
    • gce config service ... -profile <profileName>                      to associate a profile name with a particular GCE setup

    • gce config aws ... -profile <profileName>                           to configure AWS credentials for a specified GCE setup

    • gce admin autoscaling ... -profile <profileName>               to configure autoscaling for a specified GCE setup

    • gce admin executor-settings ... -profile <profileName>      to configure the Job Executor of a specified GCE setup

    • gce job ... -profile <profileName>                                       to perform job operations on a specific GCE setup


       
  • Paths to destination folders no longer need to end with a "/".
  • The IAM:GetUser AWS permission is no longer required.
  • Fetching a list of input parameters for a workflow (gce job parameters) now runs with asap as the default priority. Previously it ran with priority set to medium.

Compatibility information

The CLC Genomics Cloud Engine Command Line Tools 1.0.6 is the corresponding client for the CLC Genomics Cloud Engine 1.0.6.

We recommend running the corresponding versions of service and client. However, CLC Genomics Cloud Engine Command Line Tools 1.0.6 can be used with CLC Genomics Cloud Engine 1.0.4, and CLC Genomics Cloud Engine Command Line Tools 1.0.4 can be used with CLC Genomics Cloud Engine 1.0.6.

The CLC Genomics Cloud Engine includes the CLC Genomics Server 9.0.

Workflows to be run on the CLC Genomics Cloud Engine 1.0.6 can be designed using Workbenches compatible with CLC Genomics Server 9.0 . These are:

  • CLC Genomics Workbench 10.x
  • Biomedical Genomics Workbench 4.x
Frequently Asked Questions


CLC Genomics Cloud Engine 1.0.4

Release date: 2017-05-22

CLC Genomics Cloud Engine 1.0.4

First release
Frequently Asked Questions

Compatibility

The CLC Genomics Cloud Engine Command Line Tools 1.0.4 is the client software for the CLC Genomics Cloud Engine 1.0.4. The CLC Genomics Cloud Engine 1.0.4 includes the CLC Genomics Server 9.0. Workflows to be run on the CLC Genomics Cloud Engine 1.0.4 can be designed using Workbenches compatible with CLC Genomics Server 9.0. These are:
      • CLC Genomics Workbench 10.0.x
      • Biomedical Genomics Workbench 4.0.x

CLC Genomics Cloud Engine Command Line Tools 1.0.4

First release


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