Local development and Deployment

This guide outlines the steps to install and deploy the Workflomics web platform, a comprehensive solution implemented in TypeScript for bioinformatics workflow benchmarking.

Development Setup

Prerequisites:

Ensure you have a Postgres database and Postgrest API set up and running. For a complete setup using Docker, refer to the Deployment section below.

Environment Configuration:

Create a .env file in the project directory and configure the proxy endpoints:

API_PROXY_TARGET=http://localhost:3000
APE_PROXY_TARGET=http://localhost:4444

Installing Dependencies:

Install the required modules for the front-end:
```
npm install
```

Running the Front-End:

To start the front-end in development mode, run:
```
npm start
```

Deployment

Back-End Services:

Setup:
- Copy docker-compose.yml to the server.
- Create a .env file in the same directory and configure the necessary variables:
```
POSTGRES_PASSWORD=<password>
WF_DATA_DIR=<data directory>
```
- Note: Ports are currently hard-coded in docker-compose.yml.
Starting Services:
- To start the database, API, and RestAPE, execute:
```
docker compose --env-file .env up -d
```
- To remove the containers, run:
```
docker compose down
```

Nginx Configuration:

The front-end requires a reverse proxy, for which Nginx can be used. A sample Nginx configuration is available in the nginx folder. Ensure it points to the correct back-end services and is symlinked from /etc/nginx/sites-available to /etc/nginx/sites-enabled.

Building and Deploying the Front-End:

Build Application:
- Ensure you’re on the correct branch and have incorporated all desired changes. Build an optimized version of the application with:
```
npm run build
```
- This command generates the application in the build directory, ready for static serving.
Serving Application:
- For serving with Nginx, copy the contents of the build/ directory to the Nginx serving directory, e.g., /var/www/workflomics.org/.

This guide provides a comprehensive approach to both developing and deploying the Workflomics platform, ensuring a smooth setup for your bioinformatics workflow benchmarking needs.