The Illumina NextSeq 1000/2000 On-Prem Integration Package v1.0.0 supports the integration of Clarity LIMS to NextSeq 1000/2000 instruments.
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
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
âš 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 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:
Use the following instructions to install the integration package. Install RPM Package
Log in using the admin credentials.
Run the following command to install the ClarityLIMS-NextSeq1k2k-OnPremise RPM package from the repository:
Run Configuration Scripts
Make sure that you are using the glsjboss user credentials.
Run the following script to set properties in the Clarity LIMS database:
After running this script, the following prompts display:
For more information about the properties set by this script and how to modify them, refer to .
Start the Sequencing Service
Log in as the root or glsjboss user.
Run the following command to start the sequencing service:
Run the following command to check the status of the integration service:
After the sequencing service starts, the following files are created at /opt/gls/clarity/extensions/nextseq1k2k-onprem:
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.
Refer to 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.
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.
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
/usr/lib/systemd/system/nextseq1k2k-onprem.service
The file used by systemid to start and stop the integration service.
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.
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.
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.
Service unit file
dnf install ClarityLIMS-NextSeq1k2k-OnPremise/opt/gls/clarity/config/configure_nextseq1k2k_onprem.shsystemctl start nextseq1k2k-onpremsystemctl status nextseq1k2k-onprem