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 Technical Requirements.
You have installed and configured the required components. For more information, 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.
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:
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:
Run the install command:
Type y to download and install the Clarity LIMS RPM core components.
NOTE: The installation of Clarity LIMS creates 3 operating system users:
glsai - User created 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 of the above users should be set by the root user.
The generated SSH key must be in PEM encoded RSA private key format for Automation scripts that require glsai user to access to another server instance using SSH key. The SSH public key file should begin with:
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 #configuration-script.
Run the following script:
Run the next script to initialize the database and overwrite any existing data:
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.
Change to the root user, and then run the following script to configure RabbitMQ:
As the root user, install the Apache proxy with the following script:
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:
Restart all Clarity LIMS services using the following command:
Make sure that LabLink is accessible at https://<your-Clarity-FQDN>/lablink
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.
Switch to the root user.
Make sure that no Clarity LIMS services are running.
Run the script with the following start command:
After the script has completed, all Clarity LIMS services should be ready for use.
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>/
The core Clarity LIMS product includes the rename_claritylims_hostname.sh script, which allows you to change the hostname to which Clarity LIMS responds.
Clarity LIMS must be fully installed and configured. If it is not, the script instructs you to complete the installation.
The script stops all Clarity LIMS services. Make sure that all automation jobs are complete.
If you are not using a wild card SSL Certificate, purchase a certificate for the new hostname.
Update the hostname returned by the operating system to match the new name.
Refer to #pre-script-steps for more information.
Running the renaming script requires root access.
The script does not update the Automation Worker installation. After you have completed the renaming steps, you must reconfigure all local and remote Automation Workers.
You might need to reconfigure additional services, such as the Reporting and Sequencing services.
We recommend that you back up the database before performing the following renaming steps.
The following table lists the settings changed by the rename_claritylims_hostname.sh script.
*The ftp.host is only updated if it matches the previous IP address/hostname. This intended behavior accounts for the scenario in which the ftp host is on a different server.
Change the internal hostname
Before running the rename_claritylims_hostname.sh script, change the internal hostname for the instance - that is, /etc/hosts and related areas. There is no need to change any other LIMS-related components.
The new internal hostname will be used in the renaming process.
To verify the internal hostname, use the following command:
NOTE: If the hostname command does not return the correct new name, consult with your IT department to correct the name.
Verify SSL Certificate path:
The script may prompt you for the SSL Certificate path. Be sure to have that ready.
Use the following command to change to the root user:
Navigate to the /opt/gls/clarity/config directory.
Run the rename_claritylims_hostname.sh script:bash rename_claritylims_hostname.sh
If prompted for your SSL Certificate path, enter this information.
The script prompts you to confirm that you have changed the internal hostname.
If you enter no, you will be prompted to manually change the hostname (output shown below).
If you enter yes, the script proceeds to modify Clarity LIMS-related components to use the new hostname.
When the renaming is complete, the script prompts you to restart Clarity LIMS by running the run_clarity.sh script:
When all Clarity LIMS services have restarted, make sure that the hostname has been changed successfully. Complete the following steps:
Connect to all system components.
Log in and test the LIMS user interface in your web browser.
This section describes the installation steps required for installing Secret Utility and integration packages.
As of Clarity LIMS v5.4, the method used for managing passwords (secrets) for Clarity LIMS integration modules has changed.
The following diagram shows the installation steps required for installing Secret Utility and integration packages with Clarity LIMS v5.4 and later.
For details on Compatibility of Releases with Integration Modules, see Integration > Compatibility.
Install Clarity LIMS v6.3.
Install Clarity LIMS-App 6.3 and complete pending script.
Secret Utility (secretutil) is installed as part of Clarity LIMS-App 6.3 dependency, and the Secret Utility configuration is part of Clarity LIMS pending scripts.
Install Secret Utility.
In the automated installation tooling for Clarity LIMS v6.3, the installation and configuration of Secret Utility is included. No further action is necessary.
For manual installation:
Install Clarity LIMS-SecretUtil.
Configure Secret Utility by running the following script:
Refer to Guide to Secret Management for details on configuring Secret Utility.
Check usage of custom API username.
Check for any needs for custom API username, if any (eg novaseq_user). The documentation for the integration package provides the requirements for API username.
NOTE: In a typical installation, a default API username (apiuser) is used. It is not necessary to add the default apiuser username, because it is configured as part of Clarity LIMS v6.3 installation. If no custom API username is required, skip step 4 and proceed to step 5.
Configure custom API username.
If a custom API username is not required, proceed to step 5.
If a custom API username is required, configure the user/password with Secret Utility as follows. Substitute the values enclosed in double quotes with your own values, keeping the double quotes.
Example:
For a custom api username, set the key to apiusers/{custom api username}
Install integration package.
There is no change to the installation of the integration package. Follow existing installation instructions.
NOTE:
The new configuration script in the new integration package retrieves passwords directly from Secret Utility.
For BSSH access token, follow the existing setup guide. There is no change in the configuration step.
Secret Utility (secretutil) is a password management tool used to store, manage, and retrieve passwords. Secret Utility returns the passwords in plain text.
The following sections describe the configuration of Secret Utility, which is installed as part of the Clarity LIMS-SecretUtil RPM.
You may refer to the integration package installation guide for more information on installing/configuring the integration package.
If Secret Utility has not been configured, the 05_configure_claritylims_secretutil.sh script is created in the /opt/gls/clarity/config/pending folder.
To reconfigure Secret Utility:
Remove the hidden file /opt/gls/clarity/tools/secretutil/.configured
Run the Secret Utility configuration script as follows: /opt/gls/clarity/config/configure_claritylims_secretutil.sh
The following table describes the entries prompted by the configure_claritylims_secretutil.sh script.
| Prompts | Default | Description |
|---|---|---|
If Secret Utility is configured as Vault Mode, the passwords are stored and retrieved from Vault Enterprise.
To use Secret Utility and perform the following steps, you must first remote into the instance before performing any of the following steps.
To use the Vault user interface (UI) and perform the following steps, you must have the appropriate role and access control list (ACL) policies.
If Secret Utility is configured as File mode, the passwords are encrypted and stored in /opt/gls/clarity/tools/secretutil/conf/secrets.properties. Encryption is based on the CLARITYSECRET_ENCRYPTION_KEY environment variable.
To manage the passwords and perform the following steps, you must first remote into the instance.
This document describes the steps required to update the Clarity LIMS application configuration.
Two levels of user passwords are created in the Clarity LIMS system: one at the operating system level and one at the Clarity LIMS level.
Following are details on the user passwords, instructions for changing them, and instructions for updating Clarity LIMS with the new database connection details.
The following steps are only required if the passwords for glsftp and/or apiuser have been changed.
The user passwords created at the operating system level are for the glsai, glsjboss, and glsftp users.
glsai and glsjboss users:
These users have no configuration associated with them.
You may change their passwords at any time.
glsftp user:
After installation of Clarity LIMS, you can change this password. However, you must also update it in the file/vault secret store, using the Secret Management Util tool.
Change the glsftp user's password on the server.
Log in to the server as the root user.
Stop Clarity LIMS using the following command:
Go to /opt/gls/clarity/tools/secretutil.
Update the password in the secret store.
For vault-based secret storage, use either the Vault command line interface (CLI) or Vault user interface (UI) to update the password.
For file-based secret storage, use Secret Management Util to update the password as follows:
Start Clarity LIMS using the following command:
The user passwords created at the Clarity LIMS level are for the admin, facility, and apiuser users.
admin and facility users:
These users have no configuration associated with them.
You may change their passwords at any time.
apiuser user:
After installation of Clarity LIMS, you can change this password. However, you must also update it in the file/vault secret store, using the Secret Management Util.
Check for any remote Automation Workers, and take note of their locations in your network. You will need to restart these after changing the password.
Log in to the server as the root user.
Stop Clarity LIMS using the following command:
Go to /opt/gls/clarity/tools/secretutil.
Update the password in the secret store
For vault-based secret storage, use either the Vault command line interface (CLI) or Vault user interface (UI) to update the password.
For file-based secret storage, use Secret Management Util to update the password as follows:
Start Clarity LIMS using the following command:
In some circumstances (such as security breaches/compromises), the database connection details (eg, database password) are updated, which prevents Clarity LIMS from connecting to the database. You can correct this issue by updating Clarity LIMS with the new database connection details as follows.
Check for any remote Automation Workers.
Update the existing tenant with the new details.
Restart any Automation Workers.
Check for any remote Automation Workers, and take note of their locations in your network.
Log in to the server as the root user.
Stop Clarity LIMS using the following command:
Go to /opt/gls/clarity/tools/secretutil.
Update existing tenant with new details.
For vault-based secret storage, use either the Vault CLI or Vault UI to update the password.
For file-based secret storage, use the Secret Management Util to update the database password as the root user.
Start Clarity LIMS using the following command:
| Property | Global | Description | Location |
|---|---|---|---|
Enter required value for Secret Utility Mode.
vault
Configure the mode for Secret Utility. Allowed values: vault, file
Enter required value for Clarity Tenant Hostname.
localhost
Vault mode only
Configure the Tenant hostname to be used as part of the vault path.
Enter required value for Vault Engine Path.
secret
Vault Mode only
Configure the secret engine path.
Enter required value for Vault URI.
Vault Mode only
Configure the Vault Server target.
Vault Enterprise (Y/N)
N
Vault Mode only
Configure whether the Vault Server is an enterprise version.
Enter required value for Vault Namespace.
Vault Enterprise only
Configure the Vault namespace.
Enter required value for Vault Authentication Mode.
Vault Mode only
Configure the authentication method. Allowed values: token, approle
Enter required value for Vault Token.
Token Authentication only
Enter required value for Vault AppRole Role-Id.
AppRole Authentication only
Configure the AppRole role-id to use. Refer to Role ID noted during HashiCorp Vault configuration. (See #approle)
Enter required value for Vault AppRole Secret-Id.
AppRole Authentication only
Configure the AppRole secret-id to use. Refer to Secret ID noted during HashiCorp Vault configuration. (See #approle)
Enter required value for app.ftp.password
Enter required value for app.ldap.managerPass
Enter required value for app.rabbitmq.password
Enter required value for db.tenant.password
Enter required value for db.clarity.password
Enter required value for db.lablink.password
Enter required value for db.reporting.password
File Mode only
Sets the secrets (encrypted with CLARITYSECRET_ENCRYPTION_KEY env variable) into conf/secret.properties
Global values
Enter required value for platform.clientid (optional for integration with Platform Auth)
File Mode only
Sets the secrets (encrypted with CLARITYSECRET_ENCRYPTION_KEY env variable) into conf/secret.properties
Enter required value for Username for API user
apiuser
File Mode only
Sets the username of the API user to be used when applications require an API user.
Enter required password for API user
File Mode only
Sets the password for the API user configured.
namingProviderHost
Yes
Configures appropriate endpoint for the Automation Worker
/opt/gls/clarity/tomcat/current/lib/ activity-management-ui-config.groovy
api.uri
Per tenant setting
Base URI used by integrations for API calls
Property Table
ftp.host
Per tenant setting
Location of FTP host for this tenant*
Property Table
ServerName
Per tenant setting
Server name reference in lookup database
Lookup Database