Installation

The Illumina NextSeq 1000/2000 On-Prem Integration Package v1.0.0 supports the integration of Clarity LIMS to NextSeq 1000/2000 instruments.

Prerequisites

NextSeq 1000/2000 On-Prem Integration v1.0.0 has the following prerequisites:

• Illumina Preset Protocols (IPP) v2.8 or later, which contains the NextSeq 1000/2000 On-Prem Sequencing workflow

• NGS Package v5.25.0 or later, which contains automation scripts used by the workflow

• Clarity LIMS v6.2 or later with NAS shares and mount points

Prerequisite 1: IPP v2.8 and NGS v5.25.0 Installation

The NextSeq 1000/2000 On-Prem Integration v1.0.0 includes the workflows, protocols, and steps provided in IPP v2.8. The following workflows can be installed with IPP v2.8:

• NextSeq 1000/2000 On-Prem Sequencing v1.0 workflow

• [Optional] Library Prep Validation v2.3.3 workflow (recommended)

NGS v5.25.0 is also installed during the IPP installation process. For instructions, refer to Illumina Preset Protocols v2.8 Installation and User Configuration.

Prerequisite 2: Clarity LIMS with NAS Share and Mount Points

⚠️ The mount points and the on-premise Clarity instance are recommended to be co-located for optimal performance.

The following NAS shares and mount points are required to enable files to be transmitted between Clarity LIMS (v6.2 or later) and the NextSeq 1000/2000 instrument.

Sample sheet directory

• The integration copies the generated sample sheet to this folder (for example, /mnt/sample_sheet).

• If the folder is also shared with the instrument, then the copied sample sheet can be imported directly from this location.

• The glsai users need the following permissions:

  • Files — Read and Write

  • Directories — Read, Write, and Execute

Run parent directory

• This directory (for example, /mnt/run_data) is where run information is copied to by the instrument.

• Each separate sequencing run must be represented by a subdirectory within the parent directory.

• The glsjboss users need the following permissions:

  • Files — Read

  • Directories — Read and Execute

Installation

The NextSeq 1000/2000 On-Prem Integration Package v1.0.0 is distributed as the ClarityLIMS-NextSeq1k2k-OnPremise RPM package. This package must be installed on the Clarity LIMS server.

The RPM package installs the following files:

File	Location	Description
JAR file	/opt/gls/clarity/extensions/nextseq1k2k-onprem/nextseq1k2k-integration.jar	The main application that runs the integration service. The JAR file must not be run directly.
InterOp library files	/opt/gls/clarity/extensions/nextseq1k2k-onprem/interop/lib/*.so	The shared library file used to extract sequencing run metrics from run directories.
Logging configuration file	/opt/gls/clarity/extensions/nextseq1k2k-onprem/conf/log4j2.xml	The configuration file that controls how log messages are saved and displayed.
Configuration script	/opt/gls/clarity/config/configure_nextseq1k2k_onprem.sh	The script used to configure integration-related properties.
Service unit file	/usr/lib/systemd/system/nextseq1k2k-onprem.service	The file used by systemid to start and stop the integration service.

Use the following instructions to install the integration package. Install RPM Package

1. Log in using the admin credentials.

2. Run the following command to install the ClarityLIMS-NextSeq1k2k-OnPremise RPM package from the repository:

   dnf install ClarityLIMS-NextSeq1k2k-OnPremise

Run Configuration Scripts

1. Make sure that you are using the glsjboss user credentials.

2. Run the following script to set properties in the Clarity LIMS database:

   /opt/gls/clarity/config/configure_nextseq1k2k_onprem.sh

After running this script, the following prompts display:

Prompt	Step Name	Description
Automated sequencing step base name:	AUTOMATED - Sequencing Run (NextSeq 1000/2000 On-Prem	The substring that the integration service uses to find the automated sequencing run step.
Automated demultiplexing step base name:	Demultiplexing (NextSeq 1000/2000 On-Prem	The substring that the integration service uses to find the semi-automated demultiplexing step.

For more information about the properties set by this script and how to modify them, refer to Configuration Properties.

Start the Sequencing Service

1. Log in as the root or glsjboss user.

2. Run the following command to start the sequencing service:

   systemctl start nextseq1k2k-onprem

3. Run the following command to check the status of the integration service:

   systemctl status nextseq1k2k-onprem

After the sequencing service starts, the following files are created at /opt/gls/clarity/extensions/nextseq1k2k-onprem:

File	Description
beginSequencingRun.dat	Contains the list of run folders that the integration has processed in the Sequencing Started event. These run folders can be ignored.
endSequencingRun.dat	Contains the list of run folders that the integration has processed in the Sequencing Ended event. These run folders can be ignored.
analysisRun.dat	Contains the list of run folders that the integration has processed in the Analysis Started/Ended event. These run folders can be ignored.
NextSeq1k2kIntegrator.log	Log file for the NextSeq 1000/2000 integration service.

During the initial run of the integration service, it can take some time to scan the files in the run folders within the configured Run parent directory before events are processed.

Configuration Properties

Refer to Integration Properties Details for the properties installed for this integration. Depending on the modified property, the integration service may need to be restarted for the changes to take effect.