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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

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.