Installation

These instructions cover deployment of a basic production-grade Fragalysis Stack (without custom authentication).

The Fragalysis Stack application consists of a Stack and a Fragment Graph. These application rely on additional infrastructure software in order to operate, specifically: -

You can rely on our built-in infrastructure components (which come with a number of cluster pre-requisites) that are handled by our ansible-infrastructure repository, which installs the following: -

• An NGINX ingress controller and associated Network Load balancer
• A RWX storage class (AWS EFS in our case)
• Pod Security Policies
• Certificate management
• AWX (the open-source upstream distribution of RedHat’s Ansible Tower)
• A PostgreSQL database
• An optional Keycloak server.

Once the infrastructure is installed, deployment of the Graph-based fragment database and Fragalysis Stack is achieved through the use of Jobs that are configured on the infrastructure AWX server.

If you cannot install our infrastructure (i.e. you’re on a secure or limited on-prem cluster) you must provide, at the very least: -

• An NGINX ingress controller and associated Network Load balancer
• A RWX storage class (AWS EFS in our case)
• Pod Security Policies
• Certificate management

In addition to the application cluster you will need to provide an AWS S3 bucket (or buckets) from whcih you can serve the graph and stack data - the applications will not work without any background data.

What follows is a simplified guide to setting up a basic [1] deployment of the Fragalysis Stack through a number of stages: -

Requirements, images and data

• 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 (built-in infrastructure)

• Installation - Basic (Built-in Infrastructure)
  • Installing the Infrastructure (Basic)
  • Configuring AWX (Basic)
  • Deploying the Fragment Graph
  • Deploying the Stack

Installation (on-prem infrastructure)

• Installation - Basic (On-Prem Infrastructure)
  • Command-Line Requirements (Control Machine)
  • Deploying the Fragment Graph
  • Deploying the Stack
  • Example sets of variables (AWS)

Screenshots

• mArh Screenshots
  • Target List
  • Hit Navigator
  • Alternative Molecules

AWX Fundamentals

• AWX Fundamentals
  • Objects

Footnotes

[1]	A cluster with an AWX server and a Fragalysis Stack without custom credentials or backup and recovery strategies. A cluster with the ability to use the stack with publicly available graph fragment data.