DRAGEN Bio IT Platform v4 Oracle 8 upgrade instructions

Important Notes:

1. Remote upgrade (via BMC) is not supported.

2. DRAGEN v3.9.5 and above have Oracle Linux 8 specific installers.

3. DRAGEN TSO500 v2.1 (or higher) and DRAGEN TSO500 Solid v2.1.1 (or higher) have Oracle Linux 8 specific installers. Contact [e-mail] for the installers.

4. Users running older versions of DRAGEN and/or specialized workflows such as DRAGEN TSO500 Solid/ctDNA, DRAGEN Covid Pipeline must stay on CentOS 7.

Introduction

CentOS 7 is reaching end-of-life and will no longer receive maintenance and security updates after June 30, 2024. For more information, refer to the CentOS product information page.

Illumina will be discontinuing support of the CentOS 7 operating system for all DRAGEN Servers on June 30, 2024. Illumina will continue to release DRAGEN software versions compatible with CentOS 7 through June 30, 2024.

Customers with the Illumina DRAGEN Server v3 or v4 should make plans to upgrade their affected DRAGEN Servers to Oracle 8 before June 30, 2024 to continue to receive the latest DRAGEN software.

Prerequisites

• USB stick (at least 8GB) for the bootable image.

• A second USB stick for backup files.

• Identify if the server is a v3 or v4 DRAGEN server; below are pictures of a v4 server that can be used as reference. These instructions are specific to a v4 server.

  Front-side of a v4 server Back-side of a v4 server

Backup Data

Note: The re-imaging process will delete all existing files and settings from the server. Backup any user data and settings before installing the new OS.

1. Login as root.

2. Insert the USB stick for backups into the DRAGEN server.

3. To identify the USB device name, run:

$ fdisk -l  

The USB should be recognized as /dev/sdX where X is a number.

1. Create a directory to which to mount the USB.

$ mkdir /media/backupUSB  

1. Mount the backup USB.

$ mount /dev/sdX /media/backupUSB  

1. Obtain the serial number of the DRAGEN server by running the command:

$ dragen_info -b | grep 'Serial Number' | awk -F" " '{print $3}'  

1. Using the serial number, create a directory on the USB which will hold the backup files. This is not a directory naming requirement, but using the serial number is a helpful, especially if there are multiple DRAGEN servers in the lab.

$ mkdir /media/backupUSB/<SerialNumber>    

1. Change directories into the backup directory just created.

$ cd /media/backupUSB/<SerialNumber>  

1. Backup License files using this command:

$ tar -cvpf licenses.tar /var/lib/edico  

1. Backup mount points (fstab file).

$ cp /etc/fstab .  

Preparing Bootable USB

1. Download OL8 ISO. a. Verify checksum: MD5: 28d4536aec95ef48e75adc8a8aee22f3

Information on how the MD5 checksum is generated can be found here: Generating the MD5 checksum for a file

1. Prepare a dedicated bootable USB with Ventoy.

• Download the installation package from here (like ventoy-x.x.xx-windows.zip).
• On the next page, select the green button "Download latest version" to download Ventoy.

  
• Unzip/Decompress the downloaded file.

• Run Ventoy2Disk.exe, select the USB drive (8GB or larger), and select the Install button (note: these images are from the Windows version).

  
• Copy the downloaded ISO file to the USB stick (or manually drag-drop to the USB drive).

• Verify MD5 checksum for ORCL8 file from step 1.

Installation

1. Power on the server and let it boot up fully. Its important that the server boots up fully since this enables the self-encrypted drives to unlock.

2. Login as root.

3. Insert bootable USB with the OL8 image.

4. Restart the server:

$ reboot -f  

1. While the system boots up, press DELETE during boot up to enter BIOS.

2. In BIOS, go to the last tab Save & Exit; scroll down to the Boot Override section using arrow keys, and choose the USB drive UEFI: USB, Partition 2.
3. The system will open Ventoy user interface; Select Boot in normal mode, then select the Clonezilla option.

1. This will start Clonezilla; select the first option (Default settings, VGA 800x6000).

The installer runs for a few minutes, and once it installs Oracle Linux 8, it automatically reboots.

1. Remove the Ventoy USB stick from the server before the system boots up.

2. Once the system boots up (from the hard drive), select the first option, Oracle Linux Server (4.18.0-513.5.1.el8_9.x86_64) 8.9 or leave the screen as is (the first option is automatically loaded if nothing is selected in 10 seconds).

The system will reboot once this step is done.

1. Login using default root login credentials.

Username: root    
Password: Hello@Illumina!  

There will be a prompt to change the default root password at first login. 12. Run the following script.

$ /usr/local/bin/mfg_unset.sh  

Steps after Installation

1. Apply network configuration. Refer to the page 15 of the Site Prep and Installation Guide for instructions.

2. Insert the backup USB into an open USB port on the back.

3. To identify the USB name, run:

$ fdisk -l  

The USB should be recognized as /dev/sdX where X is a number 4. Create a directory to mount the USB to:

$ mkdir /media/backupUSB  

1. Mount the backup USB.

$ mount /dev/sdX /media/backupUSB  

1. Change into the USB backup directory. Make sure that the backup folder for the correct server is being used. If the serial number was used this would look like:

$ cd /media/backupUSB/[SerialNumber]  

1. Restore the DRAGEN license files.

$ tar -xvf license.tar -C /    

1. Restore the NFS and CIFS mounts from the fstab backup.

$ awk '$3 ~ /^(nfs|cifs)/' fstab >> /etc/fstab && mount -a  

1. Download and install the latest version of DRAGEN from the support site.

2. Confirm successful installation by running the DRAGEN self test.

$ /opt/edico/self_test/self_test.sh  

For DRAGEN v4.3.6 and higher, a self test can be run with the following command

$ /opt/dragen/4.3.6/self_test/self_test.sh  

If self test fails, perform a cold reboot of the server and run it again.

1. Create additional users as needed.

For any feedback or questions regarding this article (Illumina Knowledge Article #7439), contact Illumina Technical Support [e-mail].