Implementing a RedHat, Ceph, and Rook Environment for Kubernetes and Docker

When creating my Docker Images/Containers for utilizing reference and patient genomes to create Variant Call Format (VCF) Files for each chromosome of focus in precision medicine approaches, I primarily utilized AWS. In my earlier phases, I created a RedHat, Ceph, and Rook Environment for Kubernetes and Docker for early methods. I’ve had some requests about the installation workflow, so I created the process flow and diagram below. The text process flow below is at a high level, whereas the diagram goes through the process step by step.

Section 1 - Download and Getting Started Portals

Section 2 - RedHat Install Process

Getting RedHat Enterprise Linux up and running involves several systematic steps to ensure a secure and functional operating environment. From preparing your installation to disk configuration and applying necessary updates, following these steps will get you a solid base for your environment:

  1. Prepare for Installation - Ensure hardware compatibility and back up any existing data.

  2. Download RHEL - Obtain the latest version of RedHat Enterprise Linux.

  3. Create Bootable Media - Use the downloaded ISO to create a media from which to boot.

  4. Boot from Media and Start Installer - Start the installation process by booting from the media created.

  5. Installation Summary and Disk Configuration - Check the installation summary; allocate disk space with a file system optimized for system operation and Ceph storage.

  6. Set Up root Password and Create Users - Secure your system with a root password and create user accounts during installation.

  7. Finish Installation and Boot into RHEL - Complete the installation process and boot into your new operating system.

  8. Apply Updates - Check for the latest updates and patch your system using the `yum` package management commands.

Section 3 - Ethernet NICs Install Process

Integrating Ethernet Network Interface Cards (NICs) is critical for network communication within the server infrastructure:

  1. Install NICs in Servers - Power down your servers, install the NICs, and power up.

  2. Driver Installation and Configuration - Detect new NICs in BIOS, install necessary drivers, configure NICs for network communication, and verify they are operational.

  3. Network Configuration and Testing - Configure IP settings and test connections to ensure network readiness.

Section 4 - Ceph on RedHat Install Process

Ceph is an open-source software-defined storage platform:

  1. Prepare Nodes and Install Ceph Packages - Prepare your nodes for integrating Ceph and install necessary packages with `yum.`

  2. Configure and Deploy Ceph Cluster - Define and deploy the Ceph cluster, ensuring all storage daemons are active.

  3. Check Cluster Status and Manage Storage - Create and mount block device images for use within the environment.

Section 5 - Ceph Cluster Layout

Understanding the Ceph cluster layout is critical for optimizing storage management, including object storage daemons, hosts, and storage pools presented as file, object, and block storage.

Section 6 - Rook Storage Orchestration Install Process

Rook simplifies storage orchestration in Kubernetes:

  1. Install Rook and Configure CephBlockPool - Use YAML configurations to create Ceph block pool resources within Kubernetes.

  2. Create StorageClass - Link the Ceph storage to Kubernetes by creating a StorageClass resource.

  3. Verify Configuration and Persistent Volume Claims - Validate the setup and create persistent volume claims for workloads.

Section 7 - Kubernetes and Docker General Overview

Understanding Kubernetes and Docker is critical in this context:

  • Kubernetes deals with pods, services, volumes, and controllers, managing the desired state of a cluster.

  • Docker, an open-source containerization platform, automates application deployment and management via containers, using Dockerfiles as blueprints for container images.

Section 8 - Docker Images/Containers for Genomic Data

Specific Docker images such as BWAMem, Samtools Sort, and Samtools Index are used for managing genomic data, where Docker containers spin up necessary processes efficiently and securely.

Section 9 - Wrapping Up

Integrating RedHat, Ceph, and Rook lays a solid foundation for precision medicine applications. By following these installation and configuration processes, developers can create a robust environment for generating and analyzing VCF files, contributing significantly to the advances in genomics and precision medicine.