This directory contains tools for setting up and configuring dsHPC environments.

Configuration file that defines the environment settings:

{
  "environment_name": "dsHPC",
  "display_name": "High-Performance Computing for DataSHIELD", 
  "docker_stack_prefix": "dshpc",
  "base_repository": "https://github.com/isglobal-brge/dsHPC-docker.git",
  "default_api_port": 8001,
  "description": "DataSHIELD High-Performance Computing Environment"
}

Configuration Options:

• environment_name: Short name used for directories and references
• display_name: Full name shown in the setup process
• docker_stack_prefix: Prefix for Docker container and network names
• base_repository: Git repository URL to clone from
• default_api_port: Default port for the API service
• description: Brief description of the environment

Main setup script that automates the environment deployment process.

The user should have a directory with their environment configuration:

my-project/
├── environment/
│   ├── methods/
│   │   ├── commands/
│   │   └── scripts/
│   ├── python.json
│   ├── r.json
│   └── system_deps.json
└── setup-dshpc-environment.sh

Run the setup script:

./setup-dshpc-environment.sh

1. Validates the environment directory structure
2. Clones the base repository from GitHub
3. Copies user's environment configuration
4. Generates a .env file with random API key
5. Builds Docker images (optional)
6. Provides startup instructions

After running the script:

my-project/
├── environment/              # Original user config
├── dsHPC-docker/            # Cloned and configured repository
│   ├── .env                 # Generated environment variables
│   ├── environment/         # User's config copied here
│   ├── config/             # User's config copied here (if exists)
│   ├── docker-compose.yml  # Ready to use
│   └── src/                # Source code
└── setup-dshpc-environment.sh

The script generates a .env file with these variables:

# API Configuration
DSHPC_API_EXTERNAL_PORT=8001
DSHPC_API_KEY=randomly-generated-32-char-key

# Docker Stack Configuration  
COMPOSE_PROJECT_NAME=dshpc

# Logging Configuration
LOG_LEVEL=WARNING

To customize for different environments:

1. Modify environment-config.json with your settings
2. Update the base repository URL to point to your fork
3. Change naming conventions by updating the docker prefix
4. Adjust default ports and other settings

Required:

• git - for cloning the repository
• docker and docker-compose - for building and running

Optional:

• jq - for JSON parsing (has fallback)
• openssl - for secure key generation (has fallback)