README.md

RNA Sequence cluster manager

This repository will set up a Kubernetes cluster for executing an RNA Sequence pipeline, then load the data and execute the pipeline according to the structure provided.

Ansible VMWARE

export VMWARE_PROXY_HOST= export VMWARE_PROXY_PORT= export VMWARE_HOST= export VMWARE_USERNAME= export VMWARE_PASSWORD=

Ansible SSH

export SSH_COMPARTMENT_KEY export SSH_COMPARTMENT_USER

Cluster components:

• Kubernetes master
• n*Kubernetes nodes
• Persistant storage

Cluster applications

• Kubernetes dashboard
• Metrics server
• InfluxDB for monitoring
• Processing deployments
  • fastqc
  • star
  • htseq
• Sidecar deployments
  • Sequence-scheduler
  • Telegraf

Build order:

• Terraform base layer (vsphere)
  • filestore
  • master
  • nodes
• Ansible kubernetes build
  • Master
  • Nodes
• Terraform helm deploy
  • Metrics
  • Dashboard
  • InfluxDB2
  • Redis
  • FastQC, STAR, HTSeq
• Queue population
  • Download file
  • write redis data
  • init queue