Installation
Last updated
Last updated
The Illumina NovaSeq 6000 Integration v3.7.0 supports the integration between Clarity LIMS (v6.3 and later) and the NovaSeq 6000 instrument. Refer to NovaSeq 6000 Integration v3.7.0 Release Notes for updates to this integration.
Clarity LIMS is automatically stopped during installation of the RPM and will need to be restarted. The file-based and API-based integrations cannot run at the same time. When the API-based integration has finished installing, shut down Clarity LIMS and uninstall the file-based integration.
For details on installed protocols and steps, automations, generated and captured files, and rules and constraints, refer to NovaSeq 6000 Integration v3.7.0 Configuration.
For information on user interaction for each step, validating and troubleshooting the integration, refer to NovaSeq 6000 Integration v3.7.0 User Interaction, Validation and Troubleshooting.
For information on the NovaSeq 6000 instrument system, refer to the NovaSeq 6000 System Support Resources.
NovaSeq 6000 Integration v3.7.0 has the following prerequisites:
NovaSeq Integration v3.7.0 is distributed as the BaseSpaceLIMS-sequencer-api RPM package. This package must be installed on the Clarity LIMS server.
The BaseSpaceLIMS-sequencer-api RPM installs the following files and scripts:
Sequencer API WAR file
application.yml configuration file
configure_sequencer_api_proxy.sh configuration script
configure_sequencer_api_env.sh configuration script
configure_sequencer_api_application.sh configuration script
The RPM installs the Sequencer API WAR file into the same Tomcat container as Clarity LIMS. The WAR file is at
The version number can differ.
The WAR file is deployed automatically when Clarity LIMS launches. Because the RPM installs a new WAR file, Clarity LIMS is automatically stopped during installation of the RPM. Restart Clarity LIMS before installing the NovaSeq and Library Prep Validation workflow configuration from the IPP.
The application.yml configuration file is installed at
As part of the installation process, the file is configured with one of the configuration scripts.
For a complete list of all properties included in the application.yml file and the properties installed into database, refer to Integration Properties Details.
The scripts in the following table are installed at the
During installation, the RPM runs these scripts as they are needed.
If running the sequencing service and Automation Worker on the same instance, the instance must also be running a compatible version of Oracle Linux. For compatibility, refer to NovaSeq 6000 Integration v3.7.0 Release Notes.
NovaSeq 6000 Integration v3.7.0 includes the workflows, protocols, and steps listed in the following table. The workflows are found in IPP v2.9.0 package.
For detailed descriptions of the steps and automations included in each protocol, and details on other components in the configuration, refer to NovaSeq 6000 Integration v3.7.0 Configuration.
For instructions on using the Library Prep Validation v2.3.4 protocol, refer to NovaSeq 6000 Integration v3.7.0 User Interaction, Validation and Troubleshooting.
The NovaSeq instrument software includes the following components:
NovaSeq Control Software (NVCS) — Contains the user interface for setting up the sequencing run. Responsible for controlling the instrument and acquiring the images.
Real-Time Analysis v3 (RTA3) — Takes the images generated by the first module, processes, and analyzes them. Makes sure that data files are created and copied to the final destination folder.
Sequencing Analysis Viewer (SAV) — Displays the important quality metrics generated by the RTA3 software.
NovaSeq recipes — Provides system operation instructions for use with NovaSeq 6000 reagent kits for SP, S1, S2, and S4 flow cells.
Universal Copy Service — Copies output files to destinations such as final destination folder and/or BaseSpace Sequence Hub (when the instrument is configured for use with BaseSpace Sequence Hub).
For the NovaSeq API integration to work, the NovaSeq instrument must be able to communicate with Clarity LIMS through the API. Complete the following steps to configure the NVCS and confirm that you can access Clarity LIMS from the instrument.
Launch NVCS and wait for the initialization process to complete.
On the NVCS Settings page, do the following:
Under Mode Selection, select Server-Based.
In the adjacent field, enter the Clarity LIMS URL (e.g., https://customerserver.claritylims.com).
[Optional] In the Output Folder field, enter the default output folder location. You can also specify the output folder location when setting up a run in NVCS.
Select Save to complete the configuration.
On the NVCS home page, you can now select Sequence to log into Clarity LIMS and start a run.
This script modifies /opt/gls/clarity/tomcat/current/bin/setenv.sh for Clarity LIMS Tomcat to load the Secret Utility environment variable file (/etc/profile.d/claritysecret.sh) during startup.
The installer validates the import of the workflow and provides the Warning/Error details in STDOUT, which allows you to either proceed with the import or cancel it.
The configuration provided in this integration has been established to support NovaSeq 6000 lab processes. Any configuration changes to protocols or workflows, including renaming protocols, steps, and fields, could break process.
Script Name
User
Description
configure_sequencer_api_proxy.sh
root
Adds configuration to the proxy to allow communication with the Sequencer API after Tomcat has been started.
Run this script in the following scenarios:
When the Sequencer API is first installed.
When reconfiguring the Clarity LIMS proxy. This process happens until a version of Clarity LIMS that includes the necessary configuration files from /etc/httpd/clarity/*.conf is available.
configure_sequencer_api_env.sh
root
Adds Secret Management setting into the Clarity LIMS Tomcat configuration.
configure_sequencer_api_application.sh
glsjboss
Configures the installed application.yml file.
Sets the Clarity LIMS URL and the key to use when signing access tokens.
If you run the script multiple times, the script reconfigures each setting to its default.
The only exception is the signing key. For this setting, you are asked if you want a reset. If the reset is done, all previously issued tokens are no longer valid.
Not required for Illumina cloud hosted installations.
Run this script when the Sequencer API is first installed.