Clarity LIMS
Illumina Connected Software
Clarity LIMS v6.3 & Lablink v2.5
Clarity LIMS v6.3 & Lablink v2.5
  • Release Notes Clarity LIMS v6.3
    • Release Notes Clarity LIMS v6.3.1
    • Release Notes Clarity LIMS v6.3.0
  • Technical Overview
    • Technical Requirements
  • Installation
    • Installation Procedure
    • Guide to Secret Management
    • Install/Upgrade Secret Management for Integration Modules
    • Change the Clarity LIMS Hostname
    • Update Server Passwords and Database Connection Details
  • On-Premise Deployments
    • Pre-installation Requirements
      • Install a Purchased SSL/TLS Certificate
      • Configure Your HashiCorp Vault
    • On Premise to On Premise Upgrade Procedures
    • On Premise to On Premise In-place Upgrade Procedures
    • On Premise to Hosted Upgrade Procedures
    • Hosted to On Premise Upgrade Procedures
  • Administration
    • Database Cleanup Procedure
    • Backup and Restore Procedure
    • Receiving and Decrypting Cloud Backup Data
    • LDAP Integration
      • Using the LDAP Checker Tool
    • Illumina Connected Software Platform Integration
    • Clarity LIMS Log Files
    • Customize the Term Used for Projects
    • Enforcing Unique Sample Names Within a Project
    • Container Name Uniqueness
    • Configure Electronic Signatures
    • Creating Enrypted Passwords
    • Config Slicer Tool
      • Managing Configurations with Config Slicer
      • Upgrading a configuration package/manifest file for compatibility with Config Slicer v3.0.x
      • Config Slicer Use Cases
      • Troubleshooting Config Slicer
    • Audit Trail
      • Enabling, Validating and Disabling Audit Trail
    • System Settings
    • Automation Worker Nodes
      • Troubleshooting Automation Worker
  • Clarity LIMS v6.3 Reference Guide
    • Dashboards
      • Overview Dashboard
      • Projects Dashboard
    • Projects and Samples
      • Projects
      • Samples Accessioning
        • Sample List for Batch Import
        • Guidelines and Tips for Batch Sample Import
      • Assign and Process Samples
    • Lab View
      • Requeue and Rework Samples
      • Storing Sample Aliquots for Later Use
      • Modifying Completed Step Details
      • Alert Notifications
    • Configuration
      • Lab Work
        • Steps and Master Steps
          • Step Milestones
          • Derived Sample Naming Convention Tokens
        • Protocols
        • Workflows
      • Consumables
        • Reagents
          • Reagent Kit Lot Manifest for Batch Import
        • Controls
        • Instruments
        • Labels
        • Containers
      • Custom Fields
      • User Management
        • Manage User Access
        • User Roles
        • Configured Role-Based Permissions
        • User and Profile Page
      • Automations
        • Automation Trigger Configuration
        • Copy Custom Fields from Step Input to Output
        • Template Files Associated With Automations
    • Automated Quality Control
      • Configure a QC System
    • Search
      • Basic Search
      • Advanced Search
    • Genealogy View
    • System Performance
      • Queue Performance and Usability
      • Demultiplexing API Endpoint Performance
    • Terms and Definitions
  • LabLink v2.5 Reference Guide
    • Project
      • Email Notifications for Notes
    • Resource Materials & Contact Us
    • Users
    • Configuration
    • Publishing Files and Progress
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  1. Installation

Install/Upgrade Secret Management for Integration Modules

This section describes the installation steps required for installing Secret Utility and integration packages.

PreviousGuide to Secret ManagementNextChange the Clarity LIMS Hostname

Last updated 9 months ago

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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.

  1. 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.

  2. 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:

      1. Install Clarity LIMS-SecretUtil.

      2. Configure Secret Utility by running the following script:

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

        Refer to Guide to Secret Management for details on configuring Secret Utility.

  3. 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.

  4. 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.

      java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u="password" "key"

      Example:

      java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u="mypassword" "apiusers/novaseq_user"
    • For a custom api username, set the key to apiusers/{custom api username}

  5. 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.