Installation

Overview

This section describes how to install the DRAGEN StrataMap Local App on a v4 DRAGEN server.

Step 1: Download and transfer to the DRAGEN Server

1. The app installation package is made available by Illumina Support via a pre-signed URL upon request.
2. Download the file from the URL using your preferred method.

   1. If a network connection is available on the DRAGEN Server, download the file directly to the server using the following command: sudo wget <URL>
3. If downloaded to a separate device, transfer to the server one of the following ways:

   1. Transfer from a mounted network drive:

      1. Copy the installation package to a mounted network drive available to the DRAGEN Server.
      2. Copy the installation package to the /staging/ directory from the network drive. rsync /mounted-location-of-network-drive/<installation-package> /staging/
   2. Transfer via USB (general instructions):

      1. Obtain a Linux-compatible formatted USB drive and copy the installation package to it. Mount the USB drive on the DRAGEN server.

         1. Copy the installation package from the USB's mount point to the /staging/ directory.
         2. Safely unmount the USB drive from the server after the transfer is complete.
4. Check the permissions on the files downloaded, it may be necessary to give them execute permissions chmod +x app_installer.run

Note: If you are not familiar with mounting USB devices or moving files to restricted directories, work with your organization's IT team. They can help ensure the installation package is safely transferred to the DRAGEN server.

Step 2: Install the Application

1. Navigate to the installation package within the /staging/ directory: cd /staging/<installation-package>/
2. Extract the contents of the tar.gz archive containing the installation files: tar -xzvf <installation-package>.tar.gz
3. (Optional) Run the following command to install DRAGEN Application Manager 1.1.7 if it is not installed or is an incorrect version: sudo ./install_DAM_v1.1.7.run

   Follow all prompts; refer to the provided DRAGEN Application Manager user guide for questions.
4. Run the following command to install the application: sudo ./install_DRAGEN_Spatial_Transcriptome.sh
5. After successful installation, run the self-test: sudo ./run_self_test.sh

This script automatically installs:

Application package (.iapp) - The main analysis pipeline
Genome resources (.ires) - Reference genomes (hg38 and mm39)
Image resources (.ires) - Supporting image processing files

Installation time: the full installation typically takes 15–30 minutes depending on system performance.

Installation Options

These are advanced options for modified installations and reinstallations.

Option	Description
--iapp-path PATH	Specify a custom application file path
--genome-path PATH	Specify a custom genome resource path
--image-path PATH	Specify a custom image resource path
--skip-resources	Skip all resource installation
--skip-genomes	Skip genome resource installation only
--skip-images	Skip image resource installation only
--help	Display help information

Example: install the application only (skip resources):

./install_DRAGEN_StrataMap.sh --skip-resources

Verifying the Installation

After installation, verify that all components are properly installed.

Check installed applications and resources:

dragen-app-manager list | jq

Example output:

{
  "Applications": [
    {
      "Name": "DRAGEN_StrataMap",
      "Version": "2.1.0",
      "Provider": "Illumina",
      "Dependencies": {
        "Resources": [
          {
            "Name": "DRAGEN_StrataMap_hg38_mm39_Dragen11",
            "Version": "2.1.0",
            "Provider": "Illumina"
          },
          {
            "Name": "DRAGEN_StrataMap_Images",
            "Version": "2.1.0",
            "Provider": "Illumina"
          }
        ],
        "Images": []
      },
      "Type": "NEXTFLOW_DRAGEN"
    }
  ],
  "Resources": [
    {
      "Name": "DRAGEN_StrataMap_Images",
      "Version": "2.1.0",
      "Provider": "Illumina",
      "Type": "IMAGE"
    },
    {
      "Name": "DRAGEN_StrataMap_hg38_mm39_Dragen11",
      "Version": "2.1.0",
      "Provider": "Illumina",
      "Type": "DATA"
    }
  ]
}