Illumina Connected Software

DRAGEN Server App

Installation Procedure on DRAGEN Server

Downloader

A separate lightweight downloader for Windows, macOS, and Linux operating systems is available at the DRAGEN Installer Download Site.

Choose the downloader appropriate for your platform, when executed it will prompt you to provide a path to download the assets to. The required software packages will be downloaded into the dragen_pipelines directory under the path provided at the prompt. If the path provided was used for a previous execution of the downloader, any incomplete downloads will be resumed, existing files will be checksummed, and any files with invalid checksums will be re-downloaded.

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 or by copying to Network Storage which is reachable from the target DRAGEN Server.

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

Downloader System Requirements

Downloader Name
System Requirements

Heme_WGS_TO_{version}_Downloader_unix

x86_64 platform with glibc 2.25+

Heme_WGS_TO_{version}_Downloader_mac

arm64 macOS

Heme_WGS_TO_{version}_Downloader_windows.exe

64-bit Windows 10+

Expected downloaded content

  • 📂 dragen_pipelines

    • dragen-app-manager-1.0.14-1.x86_64-el8-offline.run

    • README

    • 📂 Heme_WGS_TO_4.4.4.62

      • install_Heme_WGS_TO_v4.4.4.62.run

      • Heme_WGS_TO_4.4.4.62.iapp

      • README

    • 📂 common

      • dpf-core_1.0.0.36.ires

      • dpf-templates_4.4.4.52.ires

      • dpf-docker-images_4.4.4.52.ires

      • dragen-4.4.4-12.multi.el8.x86_64.run

      • heme_wgs_to_resources_4.4.4.2.ires

      • hg38-alt_masked.cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1.ires

      • hs37d5_chr-cnv.hla.methyl_cg.methylated_combined.rna-11-r5.0-1.ires

      • variant_annotation_data-tmb_annotations-4.4.4-1.ires

Installer

Installation Requirements

DRAGEN and DRAGEN Application Manager

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.

The pipeline also requires DRAGEN Application Manager to be installed, and an installer is included. DRAGEN Application Manager configuration is controlled by the config.toml file located in /etc/dragen-app-manager directory. See DRAGEN Application Manager for additional information.

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.

  • Oracle Linux 8

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 Heme 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 Heme pipeline output.

    • Managing data storage is your responsibility.

Installation Instructions

  • Installing the Heme 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.

  • Copy the directory structure from the downloader directory to the target DRAGEN server (or a path accessible with sudo privileges)

  • Ensure the installer has the correct privileges by running chmod +x install_Heme_WGS_TO_v{version}.run

  • Launch the installer with root privileges sudo /path/to/install_Heme_WGS_TO_v{version}.run

    • If DRAGEN Application Manager is not already installed, the installer will exit and direct you to the path to the DRAGEN Application Manager installer

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 Heme pipeline can run successfully on a test dataset.

To run the self-test script, execute:

/usr/local/bin/check_Heme_WGS_TO_{version}.sh

The following output will show if installation is completed successfully.

Checking system configuration...OK!
Now running a test execution of the pipeline.
This could take up to 15 minutes...
Verifying analysis output.
Successfully validated test analysis results.
SUCCESS!
DRAGEN Heme WGS Tumor Only Pipeline is correctly configured and ready for use.

If the self-test prints a failure message, contact Illumina Technical Support, and provide the output file found in /staging/check_Heme_WGS_TO_{timestamp}.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 Heme pipeline

To uninstall the Heme pipeline, run the following command:

/usr/local/bin/uninstall_Heme_WGS_TO_{version}.sh

Executing the uninstall script removes the following assets:

  • All scripts, including:

    • run_Heme_WGS_TO_{version}.sh

    • check_Heme_WGS_TO_{version}.sh

    • uninstall_Heme_WGS_TO_{version}.sh

    • The application installed under DRAGEN Application Manager

If the uninstall script is executed with the -r or --removeResources flag, dependencies of the application being uninstalled will be removed if no other applications depend on them.

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

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

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