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Installation of v2.5.4 on Standalone DRAGEN Server

Overview

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

  1. DRAGEN TruSight Oncology 500 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 Analysis Software is installed properly

Installation Requirements

Hardware

  • DRAGEN server v3 or v4

  • Network-attached storage (NAS) with enabled mkfifo if performing analysis for the TruSight Oncology 500 High-Throughput assay

Software

The following software is required to successfully install DRAGEN TSO 500 v2.5.4:

  • Linux CentOS 7.9 operating system (or later) or Oracle Linux 8 (or later), one of which is provided on the server. Oracle Linux 8 is recommended.

  • Docker Software, see table below for minimum version needed. If sufficient Docker software is not present on the server, the TSO 500 installer will install compatible Docker software.

  • DRAGEN Server Software*, see table below for minimum version needed as the host version on the server. If sufficient DRAGEN software is not present on the server, the TSO 500 installer will install compatible DRAGEN software.

Software Dependency
Compatible
Installs

Docker

20.10 or greater

Docker 20.10.15

DRAGEN Server Software*

v3.10.x, where x >=19, v4.3+

DRAGEN Software 3.10.19

*The DRAGEN Server Software version may be higher than the DRAGEN version used by the DRAGEN TSO 500 v2.5.4 pipeline (DRAGEN v3.10.16), which is provided inside the DRAGEN TSO 500 docker image.

Permissions

Illumina recommends logging in as root user for installation, but as a non-root user for running TSO 500 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 Analysis Software and running the system check requires root privileges.

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

Compatibility with other DRAGEN pipelines

DRAGEN TSO 500 Analysis Software v2.5.4 is multi-version compatible. Multi-version compatibility refers to ability to be installed on a single DRAGEN server with software running a different version of DRAGEN software. For example, multi-version compatible pipelines running DRAGEN v4.3.6 can be co-installed on a server alongside DRAGEN TSO 500 pipelines running DRAGEN v3.10.17. For more details on DRAGEN multi-version compatibility, please visit page 7 of the DRAGEN v4.3.6 software release notes.

Software versions without multi-version compatibility referred to as single-version compatible. DRAGEN TSO 500 Analysis Software v2.5.4 will disrupt installations of single-version compatible software from the DRAGEN server. To uninstall a previous version of DRAGEN TSO 500 Analysis Software, refer to the respective guide.

Compatibility of software for co-installation with DRAGEN TSO 500 v2.5.4 on a DRAGEN server is summarized in the table below:

Software
Version
Type
Compatible

DRAGEN TSO 500

2.6.1

Multi-version

Yes*

DRAGEN TSO 500

2.6.0

Single-version

No

DRAGEN TSO 500

2.5.3 or below

Single-version

No

DRAGEN TSO 500 ctDNA

2.6.2+

Multi-version

Yes

DRAGEN TSO 500 ctDNA

2.6.1 or below

Single-version

No

DRAGEN pipelines**

4.3.6+

Multi-version

Yes

DRAGEN pipelines**

4.2 or below

Single-version

No

*DRAGEN TSO 500 Analysis Software v2.5.4 can run on a single server with another multi-version compatible DRAGEN TSO 500 Analysis Software, e.g. DRAGEN TSO 500 v2.6.1, and should be installed before v2.6.1. DRAGEN TSO 500 Analysis Software v2.5.4 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, DRAGEN WGS Heme v1.0.0 and others. Order of installation does not matter.

Installation Instructions

As a root user, perform the following steps to install DRAGEN TruSight Oncology 500 Analysis Software v2.5.4:

  1. Contact Illumina Customer Care at customercare@illumina.com 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_TSO500-2.5.4.run

MD5sum: sha256:0d871d8b93b4e535c0c1b5614c180fdb815f80764274279881c8a25a4e153160

  1. Use the following command to update the run script permission: chmod +x /staging/install_DRAGEN_TSO500-2.5.4.run

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

    1. For Docker, use the following command: sudo TMPDIR=/staging /staging/install_DRAGEN_TSO500-2.5.4.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_TSO500-2.5.4.run -- --noDockerInstall This will not install Apptainer, but will install the analysis software in the SIF container 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. Use the following command to build the DRAGEN server hash table (run time ~ 1 hr): /usr/local/bin/build-hashtable_DRAGEN_TSO500-2.5.4.sh Refer to Troubleshooting if any errors occur.

  6. Install your DRAGEN server licenses if needed:

    1. To run DRAGEN TSO 500 Analysis Software v2.5.4, 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, the list of licenses should include TSOCombined.

    2. To run analysis for the HRD add-on kit, you need TSO500_HRD license (not available in Japan). Contact Illumina Customer Care to obtain the license.

    3. 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

    4. For servers not connected to the internet, contact Illumina Customer Care at customercare@illumina.com for license information.

  7. 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 you have a license for HRD, the list should include TSO500_HRD. 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_TSO500-2.5.4.sh

The script checks that:

  • All required services are running

  • Proper Docker image is installed

  • DRAGEN TSO 500 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_<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 Analysis Software installation includes an uninstall script called uninstall_DRAGEN_TSO500-2.5.4.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

  • The dragen_tso500:2.5.4: Docker image

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

uninstall_DRAGEN_TSO500-2.5.4.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.

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