Installation and Setup

DRAGEN Single Cell RNA can be run on an OnPrem HPC using the DRAGEN in SW-mode and an Illumina Connected API Key. When running in this mode, the STAR aligner will be used instead of the DRAGEN RNA aligner.

Prerequisites

1. Access to high-performance compute with an EL8 or EL9 based operating system.
2. Your own domain which has an ICA Subscription, including the free version - ICA Basic. For more information on subscription setup, refer to the Illumina Connected Setup Guide

Generating an Illumina Connected API Key

To generate an Illumina API key, log in through the Illumina login to access Connected Home. The "API Keys" page in the left navigation menu allows you to view and manage you API keys.

To create a new API key, click the "Generate" button. Provide a name for the key, then choose to either include all workgroups or select specific workgroups that the key should have access to. Copy this generated key for inclusion in the license credential file. For more information on managing and generating API keys refer to the Connected Home support documentation.

A license credential file is used by DRAGEN in runtime to perform credential based authentication for users running DRAGEN SW-mode. DRAGEN must have access to the DRAGEN license server at runtime. To verify connectivity to the license server, you can query the health check endpoint which will return a 200 status code and a small JSON body if successful.

curl https://license.dragen.illumina.com/healthcheck/version --header 'Content-Type: application/json'
{"version":"<server version>"}

Use the generated API key to create the license credential file with the following format:

credentials-1=IlluminaPlatform
credentials-2=<user api key>

Pass the License Credential file to DRAGEN at runtime using the --lic-credentials parameter as specified below.

Installing DRAGEN

1. Download one of the following DRAGEN SW-Mode installers using your MyIllumina account:

   1. Red Hat Enterprise Linux 8
   2. Red Hat Enterprise Linux 9
2. Execute the .bin installer in a EL8 or EL9 based operating systems to install DRAGEN SW-mode.
3. Run DRAGEN SW-mode with the following options:

   1. --lic-credentials pointing to the license credentials file containing the Illumina Connected API key
   2. STAR aligner specific options as specified in DRAGEN documentation: STAR Aligner