Installation

Before installing Variant-Linker, ensure you have Node.js and npm (Node Package Manager) installed on your system.

Prerequisites

• Node.js: Version 14.0 or higher
• npm: Usually comes with Node.js installation
• Git: For cloning the repository

Installation Steps

1. Clone the Repository

git clone https://github.com/berntpopp/variant-linker.git
cd variant-linker

2. Install Dependencies

npm install

3. Link the Package Globally (Optional but Recommended)

This step allows you to use variant-linker command from anywhere in your system:

npm link

After linking, you can use the tool globally:

variant-linker --variant "rs6025" --output JSON

4. Verify Installation

Test your installation by running a simple variant analysis:

# If you linked globally
variant-linker --variant "rs6025" --output JSON

# Or run directly from the project directory
node src/main.js --variant "rs6025" --output JSON

If the installation was successful, you should see JSON output with variant annotation data.

Alternative Installation Methods

Using npm (Future Release)

Once published to npm, you'll be able to install Variant-Linker directly:

# Global installation
npm install -g variant-linker

# Local installation for use as a library
npm install variant-linker

Docker Installation (Future Support)

Docker support is planned for future releases, which will provide an isolated environment with all dependencies pre-configured.

Troubleshooting

Common Issues

Node.js Version Issues If you encounter errors related to Node.js version compatibility, ensure you're using Node.js 14.0 or higher:

node --version

Permission Issues on macOS/Linux If you encounter permission errors during global linking, you may need to use sudo:

sudo npm link

Network Issues If you experience network-related errors during installation, try:

npm install --registry https://registry.npmjs.org/

Missing Dependencies If some dependencies fail to install, try clearing the npm cache and reinstalling:

npm cache clean --force
rm -rf node_modules
npm install

Development Installation

If you plan to contribute to Variant-Linker development:

# Clone the repository
git clone https://github.com/berntpopp/variant-linker.git
cd variant-linker

# Install dependencies
npm install

# Run tests to ensure everything works
npm test

# Run linting
npm run lint

Next Steps

Now that you have Variant-Linker installed, check out the CLI Usage Guide to learn how to use the tool effectively.