Installation of TSO 500 ctDNA v2.6.2 on Standalone DRAGEN Server

*DRAGEN TSO 500 Analysis Software v2.6.1 can run on a single server with another multi-version compatible DRAGEN TSO 500 Analysis Software, e.g. DRAGEN TSO 500 v2.5.4, and should be installed after v2.5.4. DRAGEN TSO 500 Analysis Software v2.6.1 can be co-installed with multi-version compatible DRAGEN TSO 500 ctDNA Analysis Software or other DRAGEN pipelines with any order of installation.

**For example, DRAGEN Enrichment, DRAGEN Germline, and others. Order of installation does not matter.

Installation Instructions

Pre- and Post- Installation Steps

1. Uninstall all existing single-version compatible software on the server (see table above)

2. Install DRAGEN TSO 500 ctDNA Analysis Software v2.6.2

   • This step will disrupt previously installed single-version compatible software but will not impact multi-version compatible ones (see table above)

3. Install other multi-version DRAGEN software/pipelines if needed

   • Multi-version software can be installed in any order

Steps to Install DRAGEN TSO 500 ctDNA Analysis Software v2.6.2

As a root user, perform the following steps to install DRAGEN TSO 500 ctDNA Analysis Software v2.6.2:

1. Contact Illumina Customer Care at [e-mail] to obtain the DRAGEN TSO 500 ctDNA 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 prevents 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-2.6.2.run

MD5sum value: sha256:fb88b215f5f1077e9bff2cc153c739060a0f29c359523f4f9cbe36eb3258a85c

1. Use the following command to update the run script permission: chmod +x /staging/install_DRAGEN_TSO500_CTDNA-2.6.2.run

2. Use the following command to run the installation script (run time ~ 20 minutes):

   1. For Docker, use the following command: sudo TMPDIR=/staging /staging/install_DRAGEN_TSO500_CTDNA-2.6.2.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-2.6.2.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 may 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 log back in.

5. Install your DRAGEN server licenses if needed:

   1. To run DRAGEN TSO 500 ctDNA Analysis Software v2.6.2 , 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/dragen/3.10.19/bin/dragen_lic command.

   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/dragen/3.10.19/bin/dragen_lic -i auto

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

6. After installing DRAGEN server licenses, generate a list of installed 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-2.6.2.sh

The script checks that:

• All required services are running

• Proper Docker image is installed

• DRAGEN TSO 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 TSO 500 ctDNA Analysis Software installation includes an uninstall script called uninstall_DRAGEN_TSO500_CTDNA-2.6.2.sh, which is located in /usr/local/bin.

Executing the uninstall script removes the following assets:

• All DRAGEN TSO 500 Analysis Software related scripts located in /usr/local/bin

• Resources found in /staging/illumina/DRAGEN_TSO500_CTDNA-2.6.2

• The dragen_tso500_ctdna Docker image

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

uninstall_DRAGEN_TSO500_CTDNA-2.6.2.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.