Installation

Mounting the NAS share of run data is needed to capture and generate files associated with the sequencing run. To mount NAS shares that contain data from the Clarity LIMS server, set up the following Write privileges as the glsai user:

• Sample sheet directory — This directory is where the Prepare Files for NovaSeq script writes sample sheets.

• Run recipe directory — This directory is where the Prepare Files for NovaSeq script writes run recipe files in the JSON format.

Set up the Read privileges as the glsjboss and glsai users (or as the entire claritylims group) for the run output directory. This directory is where the sequencing service looks for run folders. The run folders must be in this directory. The service does not search sub-directories.

The sample sheet, run recipe, and run output directories can be configured independently and do not have to be on the same mount or share.

The Clarity LIMS installation tooling configures the Secret Util installation. No additional configuration is necessary. For more information on Secret Utility configuration, refer to the [Clarity LIMS (Clarity & LabLink Reference Guide) documentation](../../../clarity-lims/clarity-and-lablink.md).

1. On the Clarity LIMS server, log in as the root user.

2. Run the following yum commands to install the RPMs:

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   yum install BaseSpaceLIMS-novaseq-extensions --enablerepo=<< repo name info from support >>
   yum install BaseSpaceLIMS-novaseq-sequencing-service --enablerepo=<< repo name info from support >>

3. Enter y to confirm that you want to proceed with the RPM installations.

4. If Secret Util is not installed or configured, you must configure it before proceeding. As the glsjboss user, run the following script:

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   bash /opt/gls/clarity/config/pending/05_configure_claritylims_secretutil.sh

   For more information on installing Secret Util with the Integration Module, refer to Install/Upgrade Secret Management for Integration Modules in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

   In the configuration, make sure the system passwords are configured correctly in File mode.

5. [Optional] If you are upgrading from a previous integration, check for any usages of the Custom API Username in the current system as follows.

   1. Install ClarityLIMS-UpgradePreValidation.

   2. Check for any custom API username requirements (e.g., novaseq_user).

      Typically, the default API user name is apiuser.

   3. Run the following script:

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      /opt/gls/ClarityUpgradeValidation/bin/checkUsernameConfiguration.sh

   4. After the script is complete, check that a custom user is configured in the results.

      If a custom API username is configured, a warning message displays.

   5. If a custom API username is required, configure the username and password using Secret Util:

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      java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u= 

      For a custom API username, set the to apiusers/{custom API username} (e.g., apiusers/novaseq_user). For more information on Secret Utility configuration, refer to the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

   6. Use the following command to make sure that the password is saved correctly in Secret Util:

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      java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION 

1. As the glsjboss user, use the following command to run the configure_extensions_novaseq.sh script:

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   bash /opt/gls/clarity/config/configure_extensions_novaseq.sh

2. When prompted, enter the channel name for the Automation Worker and sequencing service.

When upgrading from NovaSeq Integration v2.2.0 to v2.5.0, a conflict is expected during the workflow import with the Flowcell Type analyte custom field due to SP being added to the list of preset values. You can manually add SP as one of the values of the Flowcell Type custom field after you import the workflow.

To enable capture and generation of files associated with the sequencing run, configure the properties using the omxProps-ConfigTool utility.

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

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   systemctl start novaseq_seqservice

The following hardware, operating system, and network specifications must be met to install the BaseSpaceLIMS-novaseq-sequencing-service RPM:

• Hardware requirements:

  • 64-bit processor (dual core 2.0 GHz)

  • OS requirements, plus at least an additional 2 GB RAM

  • A minimum of 5 GB of hard disk space

• Operating system requirements:

  • Clarity LIMS v6.2 or later

  • Oracle Linux (for compatibility, refer to NovaSeq 6000 Integration v2.5.0 Release Notes)

  • Minimum requirements for remote Automation Worker (for more information, refer to the Clarity LIMS (Clarity & LabLink Reference Guide) documentation)

• Network requirements:

  • SSL access to the Clarity LIMS server from the network

  • The mounted folder where the run recipes are written

  • The mounted folder where the sample sheets are written

  • The mounted folder where the sequencing runs are written

1. On the applicable server, log in as the root user.

2. Run the following yum command to install the BaseSpaceLIMS-novaseq-extensions RPM:

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   yum install BaseSpaceLIMS-novaseq-extensions --enablerepo=<< repo name info from support >>

3. Enter y to confirm that you want to proceed with the RPM installation.

4. If Secret Util is not installed or configured, you must configure it before proceeding. As the glsjboss user, run the following script:

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   bash /opt/gls/clarity/config/pending/05_configure_claritylims_secretutil.sh

   For more information on installing Secret Util with the Integration Module, refer to Install/Upgrade Secret Management for Integration Modules in the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

5. [Optional] If a custom API username is required, configure the username and password as follows.

   1. Run the following command using Secret Util:

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      java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION -u= 

      For a custom API username, set the to apiusers/{custom API username} (e.g., apiusers/novaseq_user). For more information on Secret Utility configuration, refer to the Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

   2. Use the following command to make sure that the password is saved correctly in Secret Util:

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      java -jar /opt/gls/clarity/tools/secretutil/secretutil.jar -n=INTEGRATION 

1. As the glsjboss user, use the following command to run the configure_extensions_novaseq.sh script:

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   bash /opt/gls/clarity/config/configure_extensions_novaseq.sh

2. When prompted, enter the channel name for the Automation Worker and sequencing service. The recommended channel name is remotens. For more information, refer to Update Channel Name.

When upgrading from NovaSeq Integration v2.2.0 to v2.5.0, a conflict is expected during the workflow import with the Flowcell Type analyte custom field due to SP being added to the list of preset values. You can manually add SP as one of the values of the Flowcell Type custom field after you import the workflow.

The configure_extensions_novaseq.sh script prompts for a channel name and sets the name on the following preconfigured automations:

• Prepare Files for NovaSeq (configured on Dilute and Denature (NovaSeq 6000 v2.3) and Load to Flowcell (NovaSeq 6000 v2.3) steps)

• Read InterOp Metrics (configured on AUTOMATED NovaSeq Run (NovaSeq 6000 v2.3) step)

If you need to change the channel name, you must update it manually on each automation. The import script does not update this setting.

To enable capture and generation of files associated with the sequencing run, configure the properties using the omxProps-ConfigTool utility.

1. On the applicable server, log in as the root user.

2. Run the following yum command to install the RPM:

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   yum install BaseSpaceLIMS-novaseq-sequencing-service

3. Enter y to confirm that you want to proceed with the RPM installation.

1. Run the following script to set up the API connection properties file at /opt/gls/clarity/automation_worker/conf/api-access.properties:

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   bash /opt/gls/clarity/automation_worker/node/bin/configure.sh

The configure.sh script is provided by BaseSpaceLIMS-AutomationWorker.

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

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   systemctl start novaseq_seqservice

Steps:

1. Define Run Format (NovaSeq 6000 v2.3)

Steps:

1. Make Bulk Pool for NovaSeq Standard (NovaSeq 6000 v2.3)

2. Dilute and Denature (NovaSeq 6000 v2.3)

Steps:

1. Make Bulk Pool for NovaSeq Xp (NovaSeq 6000 v2.3)

2. Dilute, Denature & ExAmp (NovaSeq 6000 v2.3)

3. Load to Flowcell (NovaSeq 6000 v2.3)

Steps:

1. AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3)

Steps:

1. NovaSeq Validation Library Prep (NovaSeq 6000 v2.3)

Refer to the following examples for the configuration of the instrument control software:

• Sample sheet directory: \\nas\novaseq\sample_sheets

• JSON run recipes directory: \nas\novaseq\run_setup

• Output directory: \nas\novaseq\runs

Refer to the following examples for the Linux server mount points on either the Clarity LIMS or sequencing service server:

• Sample sheet directory: /mnt/novaseq_sample_sheets

• JSON run recipes directory: /mnt/novaseq_run_setup

• Output directory: /mnt/novaseq_runs

Refer to the following examples for the Clarity LIMS configuration properties:

• novaseq.runSetupFolder: /mnt/novaseq_run_setup

• novaseq.sampleSheetPathPrefixSearchReplaceSuffixes: 1

• novaseq.sampleSheetPathPrefixSearch.1: \\nas\novaseq\sample_sheets

• novaseq.sampleSheetPathPrefixReplace.1: /mnt/novaseq_sample_sheets

• novaseq.seqservice.netPathPrefixSearchReplaceSuffixes: 1

• novaseq.seqservice.netPathPrefixSearch.1: \\nas\novaseq\runs

• novaseq.seqservice.netPathPrefixReplace.1: /mnt/novaseq_runs

The following examples assume the same configuration and mount points from the previous sections.

After completing the Dilute and Denature (NovaSeq 6000 v2.3) or Load to Flowcell (NovaSeq 6000 v2.3) step, an automated script copies the run recipe JSON file and sample sheet to the appropriate network locations. For example, a library tube or flow cell with the barcode AA12345-NNN would have the following directory content:

• /mnt/novaseq_run_setup/AA12345-NNN.json (run recipe file)

• /mnt/novaseq_sample_sheets/AA12345-NNN.csv (sample sheet)

When the NovaSeq run starts, the instrument control software creates a new run folder named after the run ID. Then, the software copies the run recipe JSON file to a Clarity LIMS subfolder inside it. For example, a run ID of 170301_A001_AHHCC would have the following directory content:

• /mnt/novaseq_run_setup/AA12345-NNN.json

• /mnt/novaseq_sample_sheets/AA12345-NNN.csv

• /mnt/novaseq_runs/170301_A001_AHHCC/LIMS/AA12345-NNN.json

• /mnt/novaseq_runs/170301_A001_AHHCC/RunInfo.xml

• /mnt/novaseq_runs/170301_A001_AHHCC/RunParameters.xml

The NovaSeq 6000 sequencing service detects the run folder based on the presence of the three files inside it and starts the AUTOMATED NovaSeq Run (NovaSeq 6000 v2.3) step automatically.

After the sequencing run has completed, the Universal Copy Service copies the run data and InterOp files to the network drive. Then, the service creates a CopyComplete.txt file in the run folder. At this point, the directory would have the following content:

• /mnt/novaseq_run_setup/AA12345-NNN.json

• /mnt/novaseq_sample_sheets/AA12345-NNN.csv

• /mnt/novaseq_runs/170301_A001_AHHCC/LIMS/AA12345-NNN.json

• /mnt/novaseq_runs/170301_A001_AHHCC/RunInfo.xml

• /mnt/novaseq_runs/170301_A001_AHHCC/RunParameters.xml

• /mnt/novaseq_runs/170301_A001_AHHCC/InterOp

• /mnt/novaseq_runs/170301_A001_AHHCC/CopyComplete.txt

The NovaSeq 6000 sequencing service detects the completed sequencing run based on the presence of the CopyComplete.txt file, executes InterOp metrics parsing for the run, and automatically completes the AUTOMATED - NovaSeq Run (NovaSeq 6000 v2.3) step.