Pre-Installation Requirements

All instances of Clarity LIMS must have a purchased SSL / TLS certificate installed.

Certificate Authorities will no longer issue SSL / TLS certificates for internal server names. As a result, to obtain a certificate you must have a valid, public DNS entry for your server.

Before installing or upgrading Clarity LIMS, do the following:

For instructions on obtaining a certificate, see Install a Purchased SSL/TLS Certificate.

Security-Enhanced Linux (SELinux) is not supported for use with Clarity LIMS. Make sure that SELinux is set to either permissive or disabled mode.

For instructions, see the following sections of the Red Hat documentation:

Clarity LIMS is installed using industry standard RPM packaging. The Clarity LIMS support team requires root credentials to the server during the installation process.

The following sections discuss the system user accounts that the support team sets up during the installation process. It is important that you do not change these system users.

The production server must be configured in US locale.

Server-based User Accounts

During initial installation, the RPMs create the following server-based user accounts in a common group named claritylims.

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glsjboss—This user account is used for setting up and starting the Tomcat application server.

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glsai—This user account is used for setting up and starting the automation worker service.

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glsftp—This user account is configured to allow SFTP access and to redirect the home directory to the data storage area. The glsftp user account is used by Clarity LIMS clients to import and export files from the LIMS file server.

Do not manually create these user accounts.

During initial installation of the elastic search subsystem, the RPM creates the following server-based user account in the elasticsearch group.

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elasticsearch—This user account is used for setting up and starting the elastic search subsystem used by the LIMS search mechanism.

Do not manually create this user account.

During initial installation of the RabbitMQ subsystem, the RPM creates the following server-based user account in the rabbitmq group.

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rabbitmq—This user account is used for setting up and starting the RabbitMQ subsystem used by the search indexing mechanism.

Do not manually create this user account.

Set User Account Passwords

During the installation process, no default passwords are created for the glsjboss, glsai, and glsftp user accounts.

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Passwords must be set for these accounts.

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During execution of the Clarity LIMS installation script, you are prompted for the password of the glsftp user. Use the same password you set at the operating system level for this user.

You can find additional documentation on users at /opt/gls/clarity/documentation/users/.

Allow SSH Password-based Authentication

To enable SSH Password Authentication, add the following configuration to the /etc/ssh/sshd_config file:

Match User "glsftp"

PasswordAuthentication yes

After installing a supported database, Clarity LIMS requires certain changes to the default database configuration.

Additional tablespace names and user profiles may be needed, depending on the configuration of your system.

For more information or for assistance with your database configuration, contact the Clarity LIMS Support team.

Configure PostgreSQL Database for Use with Clarity LIMS

1.

On your database server, create a Clarity LIMS user. The Clarity LIMS user must have either full rights and permissions, or the ones defined by this command:

CREATE ROLE clarity WITH NOSUPERUSER CREATEDB NOCREATEROLE LOGIN

The Clarity LIMS user must use only the public schema. Clarity LIMS does not support other schemas.

2.

Create one database named ClarityDB and another named ClarityTenantLookup. Make sure that both databases are set up to receive remote connections from the Clarity LIMS application server.

3.

Restart PostgreSQL.

4.

Confirm the completion of these items with the Clarity LIMS Support team, and provide the following information:

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The database user name and password for both databases.

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The hostname/IP address of the database server.

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The PostgreSQL port number.

Set Up Database Maintenance Tasks

To achieve optimum performance, we recommend you perform the following database maintenance tasks, using the appropriate tools and commands.

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PostgreSQL: Routinely vacuum the database. For instructions, refer to the PostgreSQL documentation.

IPv4 support

Clarity LIMS supports only IPv4.

To access the Clarity LIMS server via DNS, make sure that the following apply:

For client systems:

Clarity LIMS requires the environment variable TZ be set on the Clarity LIMS server to your correct timezone. If the value is not configured, a default of GMT is configured by Clarity LIMS in the file /etc/profile.d/clarity.sh.

This file might update on upgrade. Any changes must be manually applied across upgrades.

To allow proper system communication, the following ports on the Clarity LIMS server must be accessible by the LIMS clients:

The following ports are required on the local Clarity LIMS server:

Computers running an automation worker must be able to reach the Clarity LIMS server via the following ports:

To facilitate instrument integrations, a site-to-site IPSEC VPN connection can be set up between your facility and the hosted instance.

There are two ports that must be opened: 4500/udp and 500/udp.

If a VPN is required, you must provide more detailed setup information to the Clarity LIMS Support team. Upon request, the Clarity LIMS Support team will provide the additional form required to do this.

Clarity LIMS uses an Apache proxy and the Clarity LIMS installation process installs and configures it automatically. If the server already has an Apache proxy installed and configured, the installation process overwrites the current configuration. If that configuration is important, you must back it up before running the Clarity LIMS installation process. Any settings that are important to your organization must be reconfigured manually after an install or upgrade of Clarity LIMS.

In Clarity LIMS v6.0.0 and later, you can choose to install and configure a HashiCorp Vault to store Clarity LIMS-related passwords and secrets safely.

For more information, refer to Configure Your HashiCorp Vault.