Installation
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The Illumina NovaSeq 6000Dx Integration v1.3.0 supports the integration between Clarity LIMS and the NovaSeq 6000Dx instrument. The integration includes the following changes:
Compatibility with Oracle Linux. For compatibility, refer to .
Security fixes. This document provides instructions for installing NovaSeq 6000Dx Integration v1.3.0 and describes the components that are installed in the default configuration.
If the user is new to the NovaSeq 6000Dx integration, then follow the instructions provided in this section. If the user has installed NovaSeq 6000Dx Integration v1.1.0, then note that there are no user-facing changes in the configured workflow between NovaSeq 6000Dx Integration v1.1.0 and NovaSeq 6000Dx Integration v1.3.0. It is safe to use the existing NovaSeq 6000Dx v1.1 workflow installed with IPP v2.5.0 and reconfigure the integration for this workflow instead. For more information, refer to [Optional] Configure Properties in .
NovaSeq 6000Dx Integration v1.3.0 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 installed to the following location:
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 to the following location:
The file properties are configured with a script during the installation process.
The scripts in the following table are installed to the following location:
During installation, the RPM runs these scripts as they are needed.
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.
ℹ Not required for Illumina cloud hosted installations.
configure_sequencer_api_env.sh
root
Adds Secret Management setting into the Clarity LIMS Tomcat configuration.
Run this script when the Sequencer API is first installed on a Secret Util-enabled Clarity LIMS.
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.
âš Run this script when the Sequencer API is first installed. 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.
NovaSeq 6000Dx Integration v1.3.0 includes the following workflows, protocols, and steps listed below. These workflows can be found in IPP v2.9.
The NovaSeq 6000Dx instrument software includes the following components:
NovaSeq 6000Dx Operating Software (NVOS) — 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 6000Dx recipes — Provides system operation instructions for use with NovaSeq 6000Dx 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 BSSH (when the instrument is configured for use with BSSH).
For the NovaSeq 6000Dx API integration to work, the instrument must be able to communicate with Clarity LIMS through the API. Complete the following steps to configure the NVOS and confirm that you can access Clarity LIMS from the instrument.
Launch NVOS and wait for the initialization process to complete.
On the NVOS Instrument Settings page, do as follows.
Select the Global Settings tab.
Under Instrument Mode, select one of the following modes:
Allow users to switch between IVD and RUO
IVD Only
RUO Only
If you selected IVD Only instrument mode, select the IVD Settings tab and complete the following steps:
Configure Run Setup as follows.
Select the Select runs from the LIMS server option.
Enter the Clarity LIMS URL (e.g., https://yourserver.claritylims.com).
[Optional] Under Output Location, enter the output folder location. You can also specify the output folder location when setting up a run in NVOS.
If you selected RUO Only instrument mode, select the RUO Settings tab and complete the following steps:
Configure Run Setup as follows.
Select the Select runs from the LIMS server option.
Enter the Clarity LIMS URL(e.g., https://yourserver.claritylims.com).
Configure Default Work Type as follows.
[Optional] If selection support between NovaSeq Xp or NovaSeq Standard is required for the workflow, select the Enable workflow selection checkbox.
Select the required default workflow type: NovaSeq Standard or NovaSeq Xp.
[Optional] Configure Output Location as follows.
[Optional] Enter the output folder location. You can also specify the output folder location when setting up a run in NVOS.
[Optional] To upload and store run data in the cloud server, select the BSSH checkbox. Select a Configuration option (Run Monitoring and Storage or Run Monitoring Only) and select your Hosting Location from the drop-down list.
Select Save to complete the configuration.
On the NVOS home page, you can now select Sequence to log into Clarity LIMS and start a run. nova
For a complete list of all properties included in the application.yml file and the properties installed into database, refer to .
If running the sequencing service and Automation Worker on the same instance, the instance must also be running a compatible version of the Oracle Linux operating system. For compatibility, refer to .
For more information on this package, refer to .
You can also press Enter to accept the default values in the application.yml configuration file. For more information about the application.yml properties, refer to .
For more information on the configurable integration properties that enable capture and generation of files associated with the sequencing run, refer to
For detailed descriptions of the steps and automations included in each protocol, and details on other components in the configuration, refer to .
For instructions on using the Library Prep Validation v2.3.4 protocol, refer to .
