Installation Procedure

This document provides the steps required to install a new BaseSpace Clarity LIMS v6.0 instance to RedHat Enterprise Linux/CentOS 7.9 operating system (OS).

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 Technical Requirements.
• You have installed and configured the required components. See Pre-Installation Requirements.
• 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 Install a Purchased SSL/TLS Certificate.
1. Using scp/sftp, WinSCP, FileZilla, PSCP, or similar, copy the repository to the following location:

/etc/yum.repos.d

2. Test the repo file with the following command:

yum --enablerepo=GLS_Clarity6 search ClarityLIMS-App

1. Run the install command:

yum --enablerepo=GLS_Clarity6 install ClarityLIMS-App

2. Type y to download and install the Clarity LIMS RPM core components.

The installation of Clarity LIMS creates the following three operating system users:

• glsai—User to run the Automation Worker node
• glsftp—User to access the SFTP file store
• glsjboss—Runs the application server

These users are created by the RPM installation process, and should not be created before starting the installation steps. The user home directories are created in the directory /opt/gls/clarity/users.

The operating system passwords for each user should be set by the root user.

1. As the glsjboss user, change directory to /opt/gls/clarity/config/pending as follows:

cd /opt/gls/clarity/config/pending

2. Run the first script listed sequentially in the directory listing.

bash /opt/gls/clarity/config/pending/05_configure_claritylims_secretutil.sh

This script configures the Secret Utility password management tool so that secrets and passwords are accessible. For more information about the prompts, see Guide to Secret Management.

For RabbitMQ:

• You must configure the password in Vault (vault mode) / File (file mode) before running the configure_rabbitmq.sh script.
• If Secret Utility is using file mode, set the RabbitMQ password as follows:

java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -u="password" app.rabbitmq.password

Using a vault is the safer way to store application secrets. If using a vault is not possible, the configuration script supports file-based storage.

3. Run the next script in the sequence, as follows:

bash /opt/gls/clarity/config/pending/20_configure_claritylims_platform.sh

4. Run the next script to initialize the database and overwrite any existing data:

bash /opt/gls/clarity/config/pending/26_initialize_claritylims_tenant.sh

This script requires that you enter the password for the glsftp user. Entering the password does not set the password for this user.

5. If your database server is standalone or remote, update the /opt/gls/clarity/tomcat/current/lib/activity-management-ui-config.groovy file with the following code snippet. Substitute the Remote DB IP and Remote DB Port placeholders with the information for your server.

hibernate {

isis {

template {

url="jdbc:postgresql://<Remote DB IP>:<Remote DB Port>/{0}"

}

}

}

If you do not update the script, log and database connection errors can occur.

6. Change to the root user, and then run the next script in the sequence to configure RabbitMQ:

bash /opt/gls/clarity/config/pending/32_root_configure_rabbitmq.sh

7. As the root user, install the Apache proxy:

bash /opt/gls/clarity/config/pending/40_root_install_proxy.sh

Before installing LabLink v2.2, make sure that a database named LabLink is created with the same database user as the Clarity LIMS database.

1. Turn off all Clarity LIMS services using the following command:

/opt/gls/clarity/bin/run_clarity.sh stop

2. Install the LabLink RPM as follows (make sure that you have the correct repo enabled):

yum --enablerepo=GLS_Clarity6 install ClarityLIMS-LabLink

3. As the glsjboss user, run the pending initialization script using the following command:

bash /opt/gls/clarity/config/pending/60_initialize_lablink.sh

The script prompts for a Google reCAPTCHA URL, site key, and secret key. If you prefer not to use reCAPTCHA, leave those fields blank. If the fields are blank, LabLink does not display the reCAPTCHA. Alternatively, you can use your own reCAPTCHA accounts when configuring LabLink.

4. Restart all Clarity LIMS services using the following command:

/opt/gls/clarity/bin/run_clarity.sh start

5. LabLink should now be accessible at the following address: https://<your-Clarity-FQDN>/lablink

Clarity LIMS includes the run_clarity.sh script. This script starts (or stops) all LIMS services (Elasticsearch, RabbitMQ, Search Indexing, Tomcat, httpd/Apache proxy, Automation Worker) in the required order, with one command.

Run the script as the root user.

/opt/gls/clarity/bin/run_clarity.sh (start|stop|restart)

If an error occurs starting any service, subsequent services will not be started. Stop all services before trying to start them again.

1. Make sure that no Clarity LIMS  services are running.

If any services are running, the script exits and provides a list of services to stop. In this scenario, complete the following steps:

a. Use the script with the stop command to stop services.
b. Open a supported browser window and make sure that you can access the LIMS client at the following URL:

https://<your-Clarity-FQDN>/

2. After the script has completed, all Clarity LIMS services should be ready for use.
3. Run the script with the start command:

/opt/gls/clarity/bin/run_clarity.sh start