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Download Connected Insights Package

Overview of Packages and Download Methods

Overview of Packages

Below are the mandatory packages needed to install Illumina Connected Insights - Local software.

  1. Connected Insights Packages — The files are downloaded from the Illumina Connected Insights Software Downloads support page using Downloader Utility.

    • Illumina Connected Insights - Local software: This is the base software package. File size: ~14 GB; file extension: .run

    • Illumina Connected Annotations: This is the Annotations sources package. File size: ~90 GB; file extension: .run

    • Illumina Connected Genome Data Reference: This is Genome references and visualization package. File size: ~11 GB; file extension: .run

  2. Connected Insights - Local software license files — These are 2 files provided to the customers by Illumina via email. Both need to be downloaded to your personal computer. One License file (ConnectedInsights-Local-SetupLicense.bin) is required to access the Connected Insights - Local software application before signing into the application and the other License File (ConnectedInsights-Local-QuotaLicense.bin) is required to add Genomic Equivalent (GE) sample credits required to perform tertiary analysis (Process Cases). Both files are mandatory to be installed.

  3. Knowledge Base files — These files are downloadable from the links provided by Illumina. Please contact connectedinsightslocal@illumina.com to receive the links.

    • JAX-CKB (File extension: .run)

    • CIViC (File extension: .run)

    • OncoKB (File extension: .run)

❗ To avoid errors during installation, make sure to not alter the names or the extensions of the downloaded files and all the files shall have execute permissions.

For downloading the packages listed in point 1, use the software Downloader Utility compatible to your download environment (Mac, Windows or Linux) from the Illumina Connected Insights Software Downloads support page. The utility shows the progress of the current package being downloaded and exits out of the terminal once downloading all the packages completes.

If the download was interrupted, the Downloader Utility can be re-executed by providing the same file path which will resume the download from where it paused previously.

Overview of Download Methods

There are 3 different ways to make the Connected Insights - Local software packages accessible on the DRAGEN v4 server. You can use any one of the below options to download and make the files accessible.

  1. Download directly to DRAGEN v4 server connected to internet

  2. Download to external storage drive mounted on the DRAGEN v4 Server using your personal computer

  3. Download and Copy Files to USB Drive

❗ Downloading all the packages on an average network speed of 300 Mbps takes between 8 to 10 hours. Downloading all the packages on the recommended network speed of 10 Gbps takes 1 to 2 hours.

Download directly to the DRAGEN Server v4 connected to internet

❗ For Linux, we currently support only Oracle Linux 8 (glibc version≥2.28 and x64), which is the base operating system installed on the DRAGEN server v4. This utility is tested only on the DRAGEN server v4 with Oracle 8 and not other flavors of Linux.

  1. Login to the DRAGEN server v4 via root or a user with sudo permissions and navigate to the /staging folder: cd /staging

  2. Download the Downloader Utility

    1. On the Chrome Browser launch Illumina Connected Insights Software Downloads support page, select View Options and then Download Utility - Unix (compatible with DRAGEN server v4).

    2. Once you click on the utility, you will be redirected to Illumina account page. Enter your valid Illumina account details. Upon successful login, when prompted, enter either your Customer Number associated with your MyIllumina Account (Or) the valid DRAGEN server v4 serial number. To get the DRAGEN server v4 serial number, login to the DRAGEN server v4 using the root or sudoer user and enter one of the following commands on the DRAGEN server v4: dragen_lic | grep Board or dragen_info -b | grep Serial. Copy the string after SN and enter it in the box prompted on the browser. This begins to download the utility which is ~8 to 10 MB in size.

  3. Once it validates, it will generate a presigned URL which is valid only for sometime. Copy this pre-signed URL if you want to directly download the files to the DRAGEN server v4 and on the command prompt enter wget "<CopiedPresignedURL>" -O ici_downloader_unix (Or) you can also download this utility on your laptop/computer and then secure copy (scp command) the utility to the DRAGEN server v4.

  4. Once downloaded, make sure the Downloader Utility has execute permission: chmod +x ici_downloader_unix

  5. Run the Downloader Utility: ./ici_downloader_unix

  6. When prompted to Please enter the path, enter: /staging. This will create the folder /icipackages under /staging and download all the Connected Insights Packages files from the support site to there.

  7. Once the Downloader Utility completes downloading, copy the Knowledge Base files (JAX-CKB, CIViC and OncoKB) received from the email link into the /icipackages folder.

  8. Make sure all the files have execute permissions. Execute these 2 commands: cd /staging/icipackages chmod +x "illumina_connected_insights_<JAX-CKB file name suffix>.run" "illumina_connected_insights_<CIViC file name suffix>.run" "illumina_connected_insights_<OncoKB file name suffix>.run"

  9. This completes the downloading step. Proceed to installing the software by following the instructions in Install Connected Insights Software.

❗ For Linux, we currently support only Oracle Linux 8 (glibc version≥2.28 and x64), which is the base operating system installed on the DRAGEN server v4. Refer to the above section.

(Or)

Download to external storage drive mounted on the DRAGEN server v4 using your personal computer

  1. Make sure the personal computer is mounted to the external storage drive directory. Also make sure that external storage drive directory is mounted to the DRAGEN server v4 as well. For details on how to mount the external storage to your laptop, refer to How to.

  2. Download the Downloader Utility from Illumina Connected Insights Software Downloads support page, select View Options and choose either Download Utility - Windows or Download Utility - Mac based on what is compatible with your download environment operating system (Mac or Windows)

  3. You will be redirected to Illumina login page. Enter your valid Illumina account details. Upon successful login, when prompted enter with your Customer Number associated with your MyIllumina Account (Or) the valid DRAGEN server v4 serial number. To get the DRAGEN server v4 serial number, login to the DRAGEN server v4 via root user and on the command prompt enter one of these commands: dragen_lic | grep Board or dragen_info -b | grep Serial. Copy the string after SN and enter it in the box prompted on the browser. Upon success, choose a location to download the utility which is about ~11 to 12MB in size.

  4. Once downloaded, make sure the Downloader Utility has execute permissions.

    • For MacOS (11.0 arm64 or higher), execute this command within the folder containing the Downloader Utility file: chmod +x ici_downloader_mac

    • For WindowsOS (Win11(x64) or higher), in File Browser, right click the Downloader Utility file, click Properties, then go to Security. Confirm the groups and users have all permissions in the Allow column ("Special permissions" not required). To add permissions, click Edit....

  5. Run the Downloader Utility.

    • For Macos (11.0 arm64 or higher), execute this command from the folder containing the Downloader Utility file: ./ici_downloader_mac

    • For WindowsOS (Win11(x64) or higher), double click on the executable (or) open Windows Command Prompt and execute the below command from the folder containing the Downloader Utility file: .\ici_downloader_windows.exe

  6. When prompted, enter the absolute file path to the mounted external storage drive directory where you want to download all the software packages.

    • Examples:

      • For MacOS (11.0 arm64 or higher): /Volumes/<Root directory of mounted external storage drive>

      • For WindowsOS (Win11(x64) or higher): \\<Root directory of mounted external storage drive>

    • This will create a folder called icipackages under the directory <Root directory of mounted external storage drive> and downloads all the software files from the support site to there. Once the download completes successfully, the Downloader Utility will exit out of the terminal.

  7. Once the Downloader Utility completes downloading, copy the Knowledge Base files (JAX-CKB, CIViC and OncoKB) received from the email link into the icipackages folder.

  8. Make sure all the files have execute permissions.

    • For MacOS (11.0 arm64 or higher), execute this command in the icipackages directory: chmod +x "illumina_connected_insights_<JAX-CKB file name suffix>.run" "illumina_connected_insights_<CIViC file name suffix>.run" "illumina_connected_insights_<OncoKB file name suffix>.run"

    • For WindowsOS (Win11(x64) or higher), the files may have execute permissions by default. To confirm or edit, see step 4 above.

  9. This completes the downloading step. Proceed to installing the software by following the instructions in Install Connected Insights Software.

(Or)

Download and Copy Files to USB Drive

Use this download method when the DRAGEN server v4 is not connected to the internet, incapable of having a personal laptop mount to it, or if the software files cannot be made available on the DRAGEN server v4 via the two methods above for other reasons.

The USB drive must meet the following requirements:

  • USB 3.0

  • At least 150 GB of storage space to accomodate all the files

  • xfs or ext4 format file system

Download the files via the USB method as follows:

  1. From your laptop which has access to the links to download all the mandatory packages, format the USB with the partition/label name as usbinstall. For instruction on how to format a USB, refer to How to section "Prepare USB compatible with DRAGEN v4 server (type xfs or ext4 only)".

  2. Download and execute the Downloader Utility on your laptop by following steps 2-5 in the section above ("Download to external storage drive mounted on the DRAGEN server v4 using your personal computer").

  3. When prompted, enter the absolute file path to either the usbinstall folder to download directly to the USB (Or) the file path to a folder on your laptop and then copy the files to the usbinstall folder once downloading completes. Once the Connected Insights Packages files are completely downloaded on/copied to usbinstall, copy the Knowledge Base files (JAX-CKB, CIViC and OncoKB) received from the email link into the usbinstall folder. For instructions on how to copy files to the USB, refer to How to under the same section "Prepare USB compatible with DRAGEN v4 server (type xfs or ext4 only)".

  4. Unplug the USB from your laptop. Take the USB and insert it into the DRAGEN v4 Server.

  5. Login to the DRAGEN v4 server as root or sudo user and create a folder named /usbinstall under the /media folder with the following command: mkdir -p /media/usbinstall

  6. Run the following command to mount the connected USB drive partition that contains the downloaded Connected Insights Packages files and Knowledge Base files to the DRAGEN server v4: mount /<path to USB partition with downloaded files> /media/usbinstall

  7. Run the following commands to make sure that the downloaded files have executable permissions: cd /media/usbinstall chmod +x *

  8. This completes the downloading step. Proceed to installing the software by following the instructions in Install Connected Insights Software.

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