Installation

The Illumina MiSeq i100 Series On-Prem Integration Package v1.0.0 supports the integration of Clarity LIMS to MiSeq i100 Series instruments that are on-premise via Illumina Run Manager.

Prerequisites

Prerequisite 1: Clarity LIMS v6.2 or later with SecretUtil v1.5.0.12 or later

The MiSeq i100 Series On-Prem integration v1.0 relies on secret management util version 1.5.0.12 or later to store the access token to Illumina Run Manager and its related secrets.

ℹ If using Vault, ensure that the appropriate ACL policies are added. Refer to Authentication ACL Policies under On-Premise Deployments > Configure Your HashiCorp Vault in Clarity LIMS (Clarity & LabLink Reference Guide) documentation.

Prerequisite 2: Illumina Run Manager Integration Service v1.0.0 or later

Illumina Run Manager Integration Service v1.0 or later is required for this integration.

Prerequisite 3: Illumina Preset Protocols (IPP) v2.10 with NGS Commons Package v5.25.0 or later

Illumina Preset Protocols (IPP) v2.10 package contains the workflow configuration and template files required to enable the MiSeq i100 Series On-Prem workflow to run properly.

Install the workflow configurations below on the same server on which you intend to install the MiSeq i100 Series On-Prem integration.

• MiSeq i100 Series On-Prem Sequencing v1.0 workflow

• Library Prep Validation v2.3.5 workflow (optional, but recommended)

NGS Commons Package v5.25.0 or later is required for Step Automation to work properly.

Installation Steps

Steps:

1. Install / Upgrade Clarity LIMS

2. Install and Configure Illumina Run Manager Integration Service

3. Install MiSeq i100 Series On-Prem Integration RPM

4. Install Illumina Preset Protocols (IPP) v2.10 RPM and Import Required IPP Workflows.

Step 1: Install / Upgrade Clarity LIMS

Install or upgrade to Clarity LIMS v6.2 or later. If you are using an older version of Clarity LIMS, please contact Illumina Support ([e-mail]) to schedule for upgrade.

Step 2: Install and Configure Illumina Run Manager Integration Service

Install and configure Illumina Run Manager Integration Service v1.0, please refer to Illumina Run Manager v1.0.0 Installation and User Interaction for details.

Step 3: Install MiSeq i100 Series On-Prem Integration RPM

Install ClarityLIMS-MiSeqi100Series-OnPremise RPM using yum or your preferred package manager.

Example with YUM:

yum install ClarityLIMS-MiSeqi100Series-OnPremise

Example with RPM:

rpm -i ClarityLIMS-MiSeqi100Series-OnPremise-{version}.86_64.rpm

Step 4: Install Illumina Preset Protocols (IPP) v2.10 and Import Required IPP Workflows

Install BaseSpaceLIMS-Illumina-Preset-Protocols RPM using yum or your preferred package manager.

Example with YUM:

yum install BaseSpaceLIMS-Illumina-Preset-Protocols

Example with RPM:

rpm -i BaseSpaceLIMS-Illumina-Preset-Protocols-{version}.86_64.rpm

Upon successful installation of IPP v2.10.0, install the following workflow configurations:

• MiSeq i100 Series On-Prem Sequencing v1.0 workflow

• (Optional) Library Prep Validation v2.3.5 workflow

For detailed options and steps on how to install IPP workflows and protocols, Installer Parameters and Operations section of Illumina Preset Protocols v2.10 Installation and User Configuration.