Getting Started

Installation Procedure on DRAGEN Server

Downloader

A separate lightweight downloader for Windows, MacOS X, and Linux platforms is available at the DRAGEN Installer Download Site.

Choose the downloader appropriate for your platform, and follow the download prompts. The required software packages will be downloaded into a designated directory and content that have been previously downloaded is cached to avoid duplication of downloaded content.

If a Windows or MacOS X downloader is chosen, the downloaded directory content may be moved to the installation target DRAGEN server using a USB key with at least 128 GB of free space.

Additional download information is available at the DRAGEN Resource Files download site.

Expected downloaded content

• <download_path>/app_installer.run

• <download_path>/dam_installer.run

• <download_path>/app_folder/

• <download_path>/common/

Installer

Installation Requirements

DRAGEN

The pipeline requires DRAGEN v4.4.4 or higher. If upon installation of the app this version of DRAGEN (or higher) is not installed, the software shall install this version of DRAGEN.

Minimum System Operating Requirements:

Hardware

• v3 DRAGEN server or v4 DRAGEN server

• mkfifo is enabled on the network-attached storage (NAS).

Software

The software installed by default on the DRAGEN server includes the following items:

• DRAGEN server software. Refer to sample sheet settings for the DRAGEN version number.

• Linux CentOS 7 and Oracle Linux 8 operating systems.

Storage

• DRAGEN server v3 provides a 6.4 TB NVMe SSD. This SSD is located at the /staging directory and is suitable for storing only one or two runs of the analysis pipeline.

• DRAGEN server v4 provides 12.8 TB via a 2 x 6.4 TB NVMe U.2 SSD configuration.

• Consider the following when making data storage decisions.

  • A NovaSeq 6000 sequencing run that uses an S4 flow cell can produce up to 3 TB of output. ▫ The pipeline can produce an additional 4-6 TB of analysis output. For optimal performance when writing to a non-default directory, specify an analysis folder location on /staging, this ensures that the DRAGEN-related processes read and write data to the DRAGEN Server's high-speed NVMe SSD.

  • Network-attached storage is required for long-term storage of sequencing runs and pipeline output.

  • Managing data storage is your responsibility.

    • Illumina recommends developing a strategy to copy data from the DRAGEN server to network-attached storage.

    • Delete output data on the DRAGEN server as soon as possible. For additional information on data output and storage, refer to Illumina Instrument Control Computer Security and Networking.

Installation Instructions

• Installing the pipeline requires root privileges.

• Contact Illumina Customer Care to request a link to the Downloader or visit DRAGEN Installer Download Site and confirm that the Genome DRAGEN license is enabled for your server.

  • Follow the instructions for DRAGEN license installation provided by Illumina Customer Care or refer to the DRAGEN server documentation.

• Store the install_DRAGEN__WGS-4.4.4.run script in the /staging directory. The script requires approximately 42 GB of free space. An additional 61 GB is needed on /staging if running with TMPDIR=/staging, or on /tmp if running without TMPDIR=/staging. Illumina recommends storing and executing the self-extracting installation script from the /staging directory.

• Update the permissions on the run script using the following command: • sudo chmod +x /staging/install_DRAGEN__WGS-4.4.4.run

• Execute the installation script depending on the targeted software container platform:

  • For Docker, use the following command:

  sudo TMPDIR=/staging /staging/ install_DRAGEN__WGS-4.4.4.run

Run Self-Test Script

The self-test script, present after app installation, checks the following functions:

• All required services are running.

• All resources are in place.

• The analysis workflow image can be launched.

• The pipeline can run successfully on a test dataset.

To run the self-test script, execute:

/usr/local/bin/check_DRAGEN__WGS-4.4.4.sh

If the self-test prints a failure message, contact Illumina Technical Support, and provide the output file found in /staging/check_DRAGEN__WGS_.tgz.

When running an analysis on the DRAGEN server via SSH, Illumina recommends that you use a terminal multiplexer utility, which allows you to resume analysis in the event of a disconnection from the DRAGEN server.

Uninstall pipeline

To uninstall the pipeline, run the following command as the root user (or with sudo privileges):

/usr/local/bin/uninstall_DRAGEN__WGS-4.4.4.sh

Executing the uninstall script removes the following assets:

• All scripts, including:

  • DRAGEN_Solid_WGS_TN_4.4.4.sh

  • check_DRAGEN_Solid_WGS_TN_4.4.4.sh

  • uninstall_DRAGEN_Solid_WGS_TN_4.4.4.sh

  • The resources found in /staging/illumina/DRAGEN_Solid_WGS_TN_4.4.4

  • The dragen_solid_wgs_tn:4.4.4 Docker image.

  You are not required to uninstall DAM, Docker or the DRAGEN server software.

  To remove Docker, review the install instructions for your operating system in the Docker documentation