Installation Procedure
This section provides instructions for installing on-premise deployments of Clarity LIMS v6.3. For assistance with installation steps, contact the Illumina Support team.
This document provides the steps required to install a new Clarity LIMS v6.3 instance to Oracle Linux/RedHat Enterprise Linux v8.10.
The installation procedure includes adding the Clarity LIMS repository, installing the Clarity LIMS RPM through yum commands, and configuring the installation through a series of configuration scripts.
Your system meets the requirements listed in .
You have installed and configured the required components. For more information, see .
You have a database user and two empty schemas on your database server. The schemas are populated during configuration.
You have received the appropriate repository files from the Clarity LIMS Support team.
All standard OS security updates have been applied.
All instances of Clarity LIMS must have a purchased SSL/TLS certificate installed. Purchase the certificate before installation or upgrade. For instructions on installing purchased SSL/TLS certificates, see .
With the Oracle Linux/RedHat Enterprise Linux server, the following error messages can display when you perform the yum commands used to install Clarity LIMS:
These messages do not affect the installation of Clarity LIMS. You can resolve these error messages by running the following command:
Step 1: Add the Clarity LIMS Repository
Using scp/sftp, WinSCP, FileZilla, PSCP, or similar, copy the repository to the following location: /etc/yum.repos.d.
Test the repo file with this command:
Step 2: Install Clarity LIMS
Type y to download and install the Clarity LIMS RPM core components.
NOTE: The installation of Clarity LIMS creates 3 operating system users:
Step 3: Run Configuration Scripts
As the glsjboss user, change directory to /opt/gls/clarity/config/pending with the following command:
Run the first script listed sequentially in the directory listing with the following bash command:
This script configures the Secret Utility password management tool so that secrets and passwords are accessible. It is recommended that you store application secrets in vault. If that is not possible, the configuration script supports file-based storage. For more information about the prompts, see .
Step 4: Install Lablink
LabLink v2.5 is compatible with Clarity LIMS v6.3.
Before installing LabLink v2.5, make sure that a database named LabLink is created with the same database user as the Clarity LIMS database.
Stop all Clarity LIMS services using the following command:
Install the LabLink RPM with the following yum command. Make sure that you have the correct repo enabled:
As the glsjboss user, run the pending initialization script using the following command:
Step 5: Start the System
Clarity LIMS includes the run_clarity.sh script. This script starts (or stops) all Clarity LIMS services (Elasticsearch, RabbitMQ, Search Indexing, Tomcat, httpd/Apache proxy, Automation Worker) in the required order, with one command.
Run the following script as the root user:
If an error occurs starting any service, subsequent services will not be started. Stop all services before trying to start them again.
Start the system as follows.
Make sure that no Clarity LIMS services are running.
Run the script with the following start command:
If any services are running, the script exits and provides a list of services to stop. In this scenario, complete the following steps:
Use the script with stop command to stop services.
Open a supported browser window and make sure that you can access the Clarity LIMS client at the following URL: https://<your-Clarity-FQDN>/