MolEvolvR Stack

This repo contains the implementation of the MolEvolvR stack, i.e.:

• frontend: the frontend web app, written in React
• backend: a backend written in Plumber
• cluster: the containerized SLURM "cluster" on which jobs are run
• services: a collection of services on which the stack relies:
  • postgres: configuration for a PostgreSQL database, which stores job information

Most of the data processing is accomplished via the MolEvolvR package, which is currently available at https://github.com/JRaviLab/molevolvr. The stack simply provides a user-friendly interface for accepting and monitoring the progress of jobs, and orchestrates running the jobs on SLURM. The jobs themselves call methods of the package at each stage of processing.

Running the Stack in Development

To run the stack, you'll need to install Docker and Docker Compose.

First, copy .env.TEMPLATE to .env and fill in the necessary values. You should supply a random password for the POSTGRES_PASSWORD variable. Of note is the DEFAULT_ENV variable, which gives run_stack.sh a default environment in which to operate; in development, this should be set to dev.

Then, you can run the following command to bring up the stack:

./run_stack.sh

This will start the stack in development mode, which automatically reloads the backend or frontend when there are changes to their source.

You should then be able to access the frontend at http://localhost:5173.

Production

To run the stack in production, you can run the following

./run_stack.sh prod

This will start the stack in production mode.