Fragalysis Stack (Kubernetes)

Preparation

• Installation
  • Cluster Requirements (AWS)
    • Cluster
    • Control Machine
  • Container Images (AWS)
    • Infrastructure Core
    • Infrastructure Database (Optional)
    • Keycloak (optional)
    • Infrastructure AWX (Optional)
    • Fragalysis Stack
    • Backup and Recovery (optional)
  • Graph and Stack data (AWS S3)
    • Graph data
    • Stack data
  • Installation - Optional Applications
    • Keycloak
    • Discourse
  • Installation - Basic (Built-in Infrastructure)
    • Installing the Infrastructure (Basic)
    • Installing AWX (Basic)
    • Configuring AWX (Basic)
    • Deploying the Fragment Graph
    • Deploying the Stack
    • Installing Monitoring (Basic)
  • Installation - Basic (On-Prem Infrastructure)
    • Command-Line Requirements (Control Machine)
    • Deploying the Fragment Graph
    • Deploying the Stack
    • Example sets of variables (AWS)
  • mArh Screenshots
    • Target List
    • Hit Navigator
    • Alternative Molecules
  • AWX Fundamentals
    • Objects
• Relocation to EKS (basic)
  • Preparation
    • Preparing for relocation
  • Installation and recovery
    • Installation and recovery
  • Deploying new stack versions
    • Updating the stack image
    • Notes for future deployments
  • Moving back
    • Moving relocated stack data back
  • Removal
    • Removing the AWS cluster

Release process

• Release process
  • Releasing stacks to staging
  • Releasing stacks to production
    • Example
• How the automated stack build works
  • Frontend
    • Changes to staging branch
    • Changes to the production branch
  • Backend
    • Changes to staging branch
    • Changes to production branch
• Release process (V1 hot-fixing)
  • Hot-fixing the f/e
  • Hot-fixing the b/e
  • Deploying a hot-fix

Architecture and development process

• Development Architecture
  • Branch and tag policy
    • Automated stack builds
    • Control variables
  • Continuous Integration
    • Fragalysis Stack Repositories
    • Build example (stack master)
    • More scenarios (here be Dragons)
    • Development Recommendation
    • Development Examples
  • Continuous Deployment
    • AWX
    • Fragalysis Stack
  • How the automated stack build works
    • Frontend
    • Backend
  • Security in Fragalysis
    • SSL/TLS
    • Authentication (who are you?)
    • Authorisation (what can you do?)
    • Access to Kubernetes
• Development Processes
  • The AWX Development Server
    • Jobs controlling the Graph Database
    • Jobs Controlling Developer Stacks
  • The AWX Production Server
    • Jobs controlling the Graph Database
    • Jobs Controlling the Production Stack
    • Jobs Controlling the Staging Stack
  • Preparing for Kubernetes Development
    • Preparing for kubectl
    • Preparing for lens
  • Cheat Sheets
    • A Developer Cheat-Sheet for kubectl
    • A Developer Cheat-Sheet for Lens
  • Deploying your Stack (“Development for Dummies”)
    • Getting started
    • Setting up GitHub Actions for CI/CD
  • Pre-release testing
    • Deploying to pre-release (staging)
    • Promoting to production
  • Building locally
  • Sensitive Material (Ansible Vault)
    • Deploying a user stack (Development Cluster)
• Backups
• Production Replication
  • Replicating to the Staging stack
  • Replication to a Developer stack

Squonk integration

• Squonk Integration
  • Configuration
    • Environment Variables
    • The Job Override
• Getting Job Definitions
• Executing a Job
  • Exposing new Jobs
    • The global section
    • The precompilation_ignore section
    • The fragalysis-jobs section

Kubernetes fragmentation process

• Fragmentation Processes
  • Architecture
  • Installation
    • Support for private-registry images
  • Running the player
    • Support for private-registry images

Administration

• Administration
  • Cloud Provider (STFC)
    • Instance base image
  • The Rancher Server
    • Cluster etcd backups
    • Cluster etcd recovery
  • Managing Cluster Access
    • Adding users
    • Managing Projects and Namespaces
    • Providing Users with access
    • Disabling a KUBECONFIG file
  • Configuring API expiry
  • The NFS Servers
    • The Dynamic Volume Server
    • The Static Media Volume Server
    • Creating the servers
    • Volume Snapshots
  • Backups
    • Rancher Server
    • Infrastructure Database (Development)
    • Infrastructure Database (Production)
    • Production Stack Database
    • Production Stack Media
  • Off-cluster backup locations
    • DLS/Echo
  • Stack Replication
    • Replication
  • AWX (Adding Developers)
    • Adding Users
    • Permissions and Duplicating Templates
    • Provide the Development Kubernetes Config file
    • Here Be Dragons!
  • Deployment Variables
    • The Stack Ansible ‘Role’
    • Role Variables (default)
    • Role Variables (vars)
  • Related Repositories
    • Informatics Matters Repositories
    • XChem Repositories
    • 3rd Party Repositories
  • Important Secrets
    • GitHub
    • DockerHub
    • PyPi
    • Deployment Secrets
  • Data Recovery
    • Stack database
    • Stack media
    • Infrastructure databases
    • Rancher server
  • Performance Considerations
    • Replicas
    • Concurrency
    • Memory and CPU Budget
  • Performance Monitoring (sysstats)
    • Collection
    • Summary
    • Playbooks
    • Displaying the summary
    • AWX
  • Ad hoc maintenance (Ansible)
  • Release process
    • Releasing stacks to staging
    • Releasing stacks to production
  • Release process (V1 hot-fixing)
    • Hot-fixing the f/e
    • Hot-fixing the b/e
    • Deploying a hot-fix