CentOS 6 is scheduled for end-of-life on November 30, 2020 and will no longer receive maintenance and security updates. Illumina is concurrently obsolescing support for the CentOS 6 operating system for Illumina software binaries and products, inclusive of DRAGEN Bio-IT Platform (DRAGEN Server and DRAGEN software) and other software such as BCL Convert.

Illumina recommends that DRAGEN Server customers with CentOS 6 as the operating system make plans to upgrade the affected DRAGEN Servers to CentOS 7 before October 31, 2020. 

This bulletin provides instructions for customers upgrading the OS on the DRAGEN server from CentOS 6 to CentOS 7. The recommended workflow is to perform a fresh install of CentOS 7 rather than attempting an upgrade in place.

Requirements

• Before beginning the upgrade process, contact Illumina Customer Service (customerservice@illumina.com) to request a DRAGEN re-installation license
  • Online customers: proceed with the instructions below after confirmation is received from Customer Service that the license security flags have been enabled for reinstallation.
  • Offline customers: run the following command from the terminal and send the output to Customer Service to confirm the current license quota usage.
    
    $ dragen_lic
    
• USB Drive (minimum 4 GB) to create a bootable OS drive.

Procedure

1. Download CentOS 7 ISO.
2. Create a bootable USB, using these instructions as a guideline.
3. Boot the CentOS 7 ISO and initiate the installation process.
   
    
   
4. Install CentOS 7.
   
    
   
5. Download and install this rpm file to enable EPEL.
6. After installation is complete, mount /dev/nvme0n1 to /staging.
   Note: This path also needs to be added to /etc/fstab.
7. Reapply any network settings.
8. Confirm that mount and network persist with reboot.
9. Download the latest version of DRAGEN from the support site.
10. Install DRAGEN using the following command:
    $ sudo sh <DRAGEN3.x.x.run>
11. Reinstall DRAGEN licenses.
    
    Online systems:
    
    $ sudo /opt/edico/bin/dragen_lic -i auto
    
    Offline systems (using the offline licenses files provided by Customer Service):
    
    $ sudo rm /var/lib/edico/*.gbin
$ sudo /opt/edico/bin/dragen_lic -i license_genome.bin
$ sudo /opt/edico/bin/dragen_lic -i license_somatic.bin
$ sudo /opt/edico/bin/dragen_lic -i license_cnv.bin
$ sudo /opt/edico/bin/dragen_lic -P license.dat
    
12. Confirm installation by running the DRAGEN Self-Test.
    
    $ /opt/edico/self_test/self_test.sh