Installation of TSO 500 ctDNA v2.6.0, v2.6.1 on Standalone DRAGEN Server

Overview

The installation script for DRAGEN TruSight Oncology 500 ctDNA Analysis Software installs the following software and dependencies:

1. DRAGEN TruSight Oncology 500 ctDNA Analysis Software itself

2. DRAGEN Software if a compatible version is not present

3. Docker software if a compatible version is not present

4. A script required to generate DRAGEN genome hash table

5. A script to check that DRAGEN TruSight Oncology 500 ctDNA Analysis Software is installed properly

Installation Requirements

Hardware

• DRAGEN server v3 or v4

Software

• By default Linux CentOS 7.9 operating system (or later) or Oracle Linux 8 (or later), is provided. Oracle Linux 8 is recommended.

• Docker Software, see table below.

• DRAGEN Software, see table below.

Software Dependency	Compatible	Installs
Docker	20.10 or greater	Docker 20.10.15
DRAGEN Software	v3.10.x where x is 17 or greater	DRAGEN Software 3.10.17

DRAGEN TruSight Oncology 500 ctDNA v2.6.0 Analysis Software is not compatible with DRAGEN Software v4.0 or above on the same standalone DRAGEN server.

Licenses

• TSO500Combined license

TSO500Combined license has been pre-installed to DRAGEN servers in manufacturing since August 2022. To generate a list of installed DRAGEN server licenses, run the following command: /opt/edico/bin/dragen_lic. If a license is not installed, contact Illumina Customer Care at [email protected] for the license.

Permissions

Illumina recommends logging in as root user for installation, but as a non-root user for running TSO 500 ctDNA analysis.

• A non-root user must be a member of the Docker group to run Docker. For more information on Docker permission requirements and alternatives to running as root, refer to the Docker documentation available on the Docker website.

• Installing and uninstalling DRAGEN TruSight Oncology 500 ctDNA Analysis Software and running the system check requires root privileges.

• Run DRAGEN TruSight Oncology 500 ctDNA Analysis Software without being logged in as a root user. Running the DRAGEN TruSight Oncology 500 ctDNA Analysis Software as root is not required or recommended.

Compatibility with other TruSight Oncology 500 ctDNA and TruSight Oncology 500 Analysis Software

DRAGEN TruSight Oncology 500 Analysis Software ctDNA v2.6.0 can be installed on one DRAGEN server with:

1. DRAGEN TruSight Oncology 500 Analysis Software v2.6.0 (v3.10.17*)

2. One prior 2.x version of DRAGEN TruSight Oncology 500 ctDNA Analysis Software (v2.1.1 (v3.10.9*), v2.5.0 (v3.10.15*), 2.6.0 (v3.10.17*), 2.6.1 (v3.10.18*))

3. One prior 2.x version of DRAGEN TruSight Oncology 500 Analysis Software (v2.1.1 (v3.10.9*), v2.5.3 (v3.10.16*)

*DRAGEN Software version

Contrary to the prior versions, the installation scripts for DRAGEN TruSight Oncology 500 ctDNA Analysis Software v2.6.0 and DRAGEN TruSight Oncology 500 v2.6.0 do not uninstall previous versions of DRAGEN TruSight Oncology 500 Analysis Software. To uninstall a previous version of DRAGEN TruSight Oncology 500 ctDNA Analysis Software, refer to the respective guide.

When installing DRAGEN TruSight Oncology 500 and DRAGEN TruSight Oncology 500 ctDNA software on the same DRAGEN server, install the software with the highest corresponding DRAGEN Software version last, as versions below v2.6.0 will overwrite with its corresponding DRAGEN Software version.

If a prior version of DRAGEN TruSight Oncology 500 ctDNA Analysis Software (eg. v2.5.0) is installed after v2.6.0, re-execute the installation script for v2.6.0 to install the compatible version of DRAGEN Software without impacting other installations.

Installation Instructions

As a root user, perform the following steps to install DRAGEN TruSight Oncology 500 ctDNA v2.6.0 Analysis Software:

1. Contact Illumina Customer Care at [email protected] to obtain the DRAGEN TruSight Oncology 500 Analysis Software installer package.

2. Download the installation package provided in the email from Illumina. The link expires after 7 days.

It is recommended to use a command line tool like wget or curl to download the file rather than pasting the link into the web browser bar. For example:

curl -o {filename} "{link}"

wget -O {filename} "{link}"

Where the file name is the installation script file name, and the link is provided by Illumina Customer Care.

1. Make sure no other analysis is being performed. Installing the software while performing other analyses prevent the installer process from proceeding.

2. Copy the install script to the /staging directory to store the script in the directory.

Installation Script:

install_DRAGEN_TSO500_ctDNA-2.6.0.run

install_DRAGEN_TSO500_ctDNA-2.6.1.run

MD5sum values v2.6.0: sha256:e98ab87152b02e2c7958f2f750fa37880a496d68e77858a09f4ad5fb07b2145b v2.6.1: sha256:026efd4402e91e8472effb30749e231817958532aae128334c5f9943564e4b8d

1. Use the following command to update the run script permission: chmod +x /staging/install_DRAGEN_TSO500_CTDNA-2.6.0.run

2. Use the following command to run the installation script, which runs for approximately 20 minutes:

   1. For Docker, use the following command: sudo TMPDIR=/staging /staging/install_DRAGEN_TSO500_CTDNA-2.6.0.run . The script installs compatible DRAGEN software and removes any previously installed versions.

   2. For Apptainer, use the following command: sudo TMPDIR=/staging /staging/install_DRAGEN_TSO500_CTDNA-2.6.0.run -- --noDockerInstall This will not install Apptainer, but will install the analysis software in the Singularity Image File (SIF) format and modify the software to launch analyses using Apptainer.

3. During the installation process, you might be instructed to reboot or power cycle the system to complete the installation of the DRAGEN software. A power cycle of the system requires the server be shut down and restarted.

4. Log out of the server and then log back in.

5. Install your DRAGEN server licenses if needed:

   1. To run DRAGEN TruSight Oncology 500 ctDNA v2.6.0 Analysis Software, you need TSOCombined license. This license is pre-installed on DRAGEN servers purchased after August 2022. To check if the license is already installed, run /opt/edico/bin/dragen_liccommand.

   2. For servers connected to the Internet, install your software licenses as follows:

      1. First, test and confirm that the server is connected to the Internet. Example: ping www.illumina.com

      2. To install the license, enter: /opt/edico/bin/dragen_lic -i auto

   3. For servers not connected to the internet, contact Illumina Customer Care at [email protected] for license information.

6. After installing DRAGEN server licenses, generate a list of installed DRAGEN server licenses by running the following command: /opt/edico/bin/dragen_lic

   If license installation is successful, the list should include TSOCombined.

   If the expected licenses are not installed, contact Illumina Customer Care.

Running the System Check

After installation is complete, make sure the system functions properly by running the following command: /usr/local/bin/check_DRAGEN_TSO500_CTDNA-2.6.0.sh

The script checks that:

• All required services are running

• Proper Docker image is installed

• DRAGEN TruSight Oncology 500 ctDNA Analysis Software can successfully process a test data set

The system check script runs for approximately 25 minutes. If the script prints a failure message, contact Illumina Technical Support and provide the /staging/check_DRAGEN_TSO500_CTDNA_<timestamp>.tgz output file.

If using MacOS to connect to a server, an error can occur if the local settings are not in English. To resolve the error, disable the ability to set environment variables automatically in Terminal settings.

Uninstall Software

The DRAGEN TruSight Oncology 500 Analysis Software installation includes an uninstall script called uninstall_DRAGEN_TSO500_CTDNA-2.6.0.sh, which is located in /usr/local/bin.

Executing the uninstall script removes the following assets:

• All DRAGEN TruSight Oncology 500 ctDNA Analysis Software related scripts located in /usr/local/bin

• Resources found in /staging/illumina/DRAGEN_TSO500_CTDNA

• The dragen_tso500_ctdna Docker image

To uninstall the DRAGEN TruSight Oncology 500 ctDNA Analysis Software, run the following command as a root user:

uninstall_DRAGEN_TSO500_CTDNA-2.6.0.sh

You are not required to uninstall Docker or DRAGEN software. To remove Docker, review the install instructions for your operating system in the Docker documentation.