On Premise to On Premise In-place Upgrade Procedures

From Clarity LIMS Version 6.2 to 6.3

This section provides the steps required to upgrade an existing on-premise deployment of Clarity LIMS v6.2 to a RedHat Enterprise Linux/Oracle Linux compatible on-premise deployment of Clarity LIMS v6.3.

For installation requirements, see Technical Requirements.

If you have questions about the upgrade procedure, contact the Illumina Support team.

Migration Paths

The following table shows the applicable migration paths.

Prerequisites

Before proceeding with the in-place upgrade from Clarity LIMS v6.2 to v6.3, note on the following:

• Your system must meet the requirements listed in .

• All standard operating system (OS) security updates must have been applied.

• The command hostname -f must resolve to the fully qualified domain name (FQDN) of the server. For details, see the section of .

Upgrade Pre-validation

To assist with validating the system before an upgrade, install the UpgradePreValidation RPM on the existing server.

• This RPM is installed temporarily, and provides tools to help check the system before an upgrade.

• If validation is successful, you can remove this RPM and proceed with the upgrade.

1. Install the UpgradePreValidation RPM.

   • As the root user, run the following command:

2. [Optional] Set up Secret Utility.

Upgrade steps

Shut Down Clarity LIMS Components

1. Determine if any of the remote automation workers (AI nodes) are running.

   • As the glsjboss user, run the following command:

     Substitute the variables as appropriate for the specific environment.

     Copy

Backup the Database and Clarity LIMS

1. Back up Postgresql database:

   On the PostgreSQL server, best practice recommends backing up the database using the pg_dump utility.

   The following example assumes the following:

   • The database server and the application server are on the same server.

Upgrade Clarity LIMS Components

1. As the root user, run the following command:

2. As the glsjboss user, run the following command:

   • This script analyzes the system and lists any required configuration steps. Make sure to carefully apply the instructions provided in the output of the scripts.

Install or Upgrade LabLink

LabLink v2.5 is compatible with Clarity LIMS v6.3.

Install LabLink 2.5

NOTE: This step is only required if installing Lablink for the first time.

Before completing the following steps, make sure that a database named lablink is created with the same database user as Clarity LIMS database.

1. Install the LabLink RPM. Make sure that you have the correct repo enabled.

   • On the instance, as the root user, run the following command:

2. Run the pending initialization script.

Upgrade LabLink 2.5

Lablink must be upgraded to the latest version if there is an order version installed.

Upgrade the LabLink RPM. Make sure that you have the correct repo enabled.

On the instance, as the root user, run the following command:

Reinstall Clarity LIMS Integration: Sequencer API RPM

NOTE: This step is only required if BaseSpaceLIMS-sequencer-api RPM is installed on the server. The RPM needs to be re-installed to resolve a known issue for version 6.3.

Run the following command to identify if the Sequencer API RPM is installed:

Use the following command to reinstall the Sequencer API RPM. Make sure that the same version is being reinstalled.

Upgrade PostgreSQL database server

Upgrade your PostgreSQL database server to v15.6. Consult a DBA to perform the upgrade.

Start the Clarity LIMS services

Use the run_clarity.sh script to start all services in the required order as follow:

• Elasticsearch

• RabbitMQ

• Search Indexing

• Tomcat

As the root user, run the following command:

• After the script has completed, all Clarity LIMS services should be ready for use.

[Optional] Upgrade Clarity LIMS Integrations

NOTE: This step is required only if Integration is needed.

Start the integration services.

• Find all the integration services and stop them, as described in the integration documentation.

Check Clarity LIMS Components

1. Determine the components that are running.

   • As the glsjboss or root user, run the following command:

     • Tomcat:

Validate the Installation

1. Log in to Clarity LIMS.

2. Make sure that Clarity LIMS is operating by performing your own validation steps.