Installation and User Interaction
Prerequisites on LIMS related configuration
Installation Steps
Follow the steps below to set up Illumina Run Manager Integration Service to connect to an Illumina instrument.
Step 1: Install/Upgrade Clarity LIMS
The Illumina Run Manager Integration Package v1.0.0 requires Clarity LIMS v6.2 or newer. If you are using an older version of Clarity LIMS and wish to upgrade to 6.2 onward, please contact Illumina Support (techsupport@illumina.com).
Step 2: Install and Configure Illumina Run Manager Integration Package v1.0.0
The installation and configuration steps are as follows:
Install the Illumina Run Manager Integration package from the repo, using root user with yum or your preferred package manager.
Example with YUM:
Example with RPM:
Switch to user glsjboss.
Run Illumina Run Manager Integration package post-installation configuration script.
Enter the details of Clarity LIMS SSL/TLS certificate configuration and complete the configuration.
Step 3: Install Supported On Premise Instrument Integration
Please refer to individual instrument integration documentations and complete the installation steps listed there.
Illumina Run Manager Integration User Interface
Connect to Instrument
Navigate to Illumina Run Manager Integration UI via the following url, https://{Clarity LIMS server url}/irm
Login with Clarity LIMS credentials (requires admin credentials).
Click "Connect Instrument" button.
On the "Connect a new instance page", select the appropriate Instrument Platform and enter the Illumina Run Manager instance URL, then click the "Connect" button.
Instrument URL refers to the hostname of the instrument. Open Terminal app on instrument, enter "hostname" and it shall return the expected value.
Enter Illumina Run Manager credential and click Sign In. Screenshot below shows NovaSeq X instrument as an example.
Upon successful connection, the Illumina Run Manager instance details will populate under the Connected Instances table.
On Clarity LIMS user interface, the registered instrument can be found under Configuration > Consumables > Instruments.
Disconnect from Instrument
Follow the steps below to disconnect an instrument:
Navigate to Illumina Run Manager Integration UI via the following url, https://{Clarity LIMS server url}/irm
Login with Clarity LIMS credentials (requires admin credentials).
Click on the delete button (trash bin icon under the "Action" column) of the Instrument Instance to be disconnected.
Click on the "Confirm" button.
On Clarity LIMS UI, manually rename the instrument (e.g. by appending prefix of "Archived_").
⚠ The system will throw an error when the user tries to connect to the same instrument again without renaming the instrument.
[Optional] Archive the disconnected instrument to avoid confusion of instruments.
Steps for instrument archival can be found in Instrument Status under Add and Configure Instruments of Clarity LIMS Reference Guide > Configuration > Consumables > Instruments in Clarity LIMS (Clarity & LabLink Reference Guide) documentation.
Reconnect to Instrument
Reconnecting an instrument is required under some circumstances (e.g., change of instrument domain name, reinstallation of Illumina Run Manager, factory reset of instrument etc.)
Follow the steps below to reconnect the instrument:
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