Illumina Genomics Architecture Workflow Installation

Illumina Genomics Architecture (IGA) workflows are included with Illumina Preset Protocols (IPP) Integration v2.2 and later. These workflows include a file-based integration with Hamilton robots that perform the various steps in handling liquids.

The IGA workflows include the Clarity LIMS workflows that run with the Hamilton robots and work with the two liquid handling methods. There is also a modified NovaSeq sequencing workflow for Clarity LIMS that has additional validation checks for the robots and the associated liquid handling methods.

When IPP and IGA workflows are installed together on a Clarity LIMS system, the following workflows are created:

• Illumina Genomics Architecture - Library Prep Automated. For more information on this workflow, refer to Illumina Genomics Architecture - Library Prep Automated v1.0.
• Illumina Genomics Architecture - NovaSeq Sequencing. For more information on this workflow, refer to Illumina Genomics Architecture - NovaSeq Sequencing v1.0.

Before you use the IGA workflows, make sure that the following items are installed:

• BaseSpaceLIMS-sequencer-api (v2.3.0.10 or later)
• Python3 (v3.6 or later), including the following dependency libraries:
– python-requests (v2.6 or later)
– python-idna (v2.4 or later)
• IPP (v2.2 or later)

The BaseSpaceLIMS-sequencer-api RPM provides an API-based integration between Clarity LIMS and the NovaSeq instrument. This RPM installs the following items:

• The SequencerAPI WAR file
• The application.yml configuration file
• The following configuration scripts:
– configure_sequencer_api_proxy.sh
– configure_sequencer_api_env.sh
– configure_sequencer_api_application.sh

To complete the installation, these scripts must be executed correctly. For more information on script configuration and the RPM installation, refer to the NovaSeq documentation in Integration & Tool Kits.

Python scripts are used frequently in automation scripts and workflow extensions (eg, V2 sample sheet generation). The IGA workflow installation requires Python3 and the python-requests (v2.6 or later) and python-idna (v2.4 or later) libraries to be installed. To install Python3 and the libraries on Clarity LIMS v6.1 and earlier, run the following command:

yum --enablerepo=centosplus install -y python3 python-requests-2.6* python-idna-2.4*

To install Python3 and the libraries on Clarity LIMS v6.2 and later, run the following command:

dnf install python2-requests

The IGA workflow installation requires the installation of IPP v2.2 or later, which also includes the Next Generation Sequencing (NGS) installation. For more information on the IPP installation, refer to the Illumina Preset Protocols documentation.

To install the IGA workflows, you must import them and update the application.yml file of SequencerAPI. This configuration update is required to make SequencerAPI compatible with the IGA NovaSeq workflow.

1. Log into Clarity LIMS as the glsjboss user.
2. Run the following command:

/opt/gls/clarity/config/illumina-preset-protocols-installer.sh -o install IGA.all

1. In the application.yml file, add the AUTOMATED - NovaSeq Run (IGA v1.0) step to the novaseq.sequenceStepNames property. The following example shows the addition of this step:

# Configuration specific to NovaSeq

novaseq:

# The list of NovaSeq sequencing step names. The names must be an exact match to the name of the step (not the master step/process type)

# Each line should be indented to the same point and start with a dash (-) like the value below.

sequenceStepNames:

- "AUTOMATED - NovaSeq Run (IGA v1.0)"

2. Restart Clarity LIMS using the following command:

/opt/gls/clarity/bin/run_clarity.sh restart