Installation

This guide covers all installation methods and system requirements for the Varvis Download CLI.

System Requirements

Required

• Node.js: v22.22.2 or higher
• NPM: v10.0.0 or higher (included with Node.js)
• Operating System: Linux, macOS, or Windows (WSL recommended)
• Memory: 512MB RAM minimum
• Storage: 100MB for tool + space for downloaded files

Optional (for Range Downloads)

These bioinformatics tools are required only for genomic range functionality:

Tool	Version	Purpose
samtools	v1.17+	BAM file processing and indexing
tabix	v1.20+	VCF file indexing and querying
bgzip	v1.20+	VCF file compression

Installation Methods

Method 1: Git Clone (Recommended)

# Clone the repository
git clone https://github.com/LaborBerlin/varvis-download.git
cd varvis-download

# Install dependencies
npm install

# Make executable
chmod +x varvis-download.js

# Test installation
./varvis-download.js --version

Method 2: Download Release

# Download latest release
curl -L https://github.com/LaborBerlin/varvis-download/archive/refs/heads/main.zip -o varvis-download.zip

# Extract and setup
unzip varvis-download.zip
cd varvis-download-main
npm install
chmod +x varvis-download.js

Method 3: Global Installation

For system-wide access:

# After cloning and installing
npm link

# Now you can use from anywhere
varvis-download --version

To uninstall:

npm unlink

Bioinformatics Tools Setup

Ubuntu/Debian

# Update package list
sudo apt update

# Install bioinformatics tools
sudo apt install samtools tabix

# bgzip is included with tabix package

CentOS/RHEL/Fedora

# Enable EPEL repository (if needed)
sudo yum install epel-release

# Install tools
sudo yum install samtools tabix

macOS

Using Homebrew:

# Install Homebrew if needed
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install bioinformatics tools
brew install samtools htslib

Windows (WSL)

# Enable WSL and install Ubuntu
wsl --install

# Follow Ubuntu instructions above

Conda/Mamba (Cross-platform)

# Create new environment
conda create -n varvis-tools samtools tabix -c bioconda

# Activate environment
conda activate varvis-tools

Verification

Verify Node.js Installation

node --version    # Should show v22.22.2+
npm --version     # Should show v10.0.0+

Verify Varvis Download CLI

./varvis-download.js --version

Expected output:

    ╭─────────────────────────────────────────────────╮
    │                                                 │
    │   ██╗   ██╗ █████╗ ██████╗ ██╗   ██╗██╗███████╗ │
    │   ██║   ██║██╔══██╗██╔══██╗██║   ██║██║██╔════╝ │
    │   ██║   ██║███████║██████╔╝██║   ██║██║███████╗ │
    │   ╚██╗ ██╔╝██╔══██║██╔══██╗╚██╗ ██╔╝██║╚════██║ │
    │    ╚████╔╝ ██║  ██║██║  ██║ ╚████╔╝ ██║███████║ │
    │     ╚═══╝  ╚═╝  ╚═╝╚═╝  ╚═╝  ╚═══╝  ╚═╝╚══════╝ │
    │                                                 │
    ╰─────────────────────────────────────────────────╯

varvis-download - Version 0.31.2
Date Last Modified: [timestamp]
Author: Bernt Popp
Repository: https://github.com/LaborBerlin/varvis-download.git
License: GPL-3.0

Verify Bioinformatics Tools

# Check tool versions
samtools --version
tabix --version
bgzip --version

# Quick functionality test
samtools view --help | head -1
tabix --help 2>&1 | head -1

Troubleshooting

Node.js Issues

Version too old:

# Check current version
node --version

# Update Node.js using NodeSource repository (Ubuntu/Debian)
curl -fsSL https://deb.nodesource.com/setup_22.x | sudo -E bash -
sudo apt-get install -y nodejs

# Or use nvm (cross-platform)
curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.0/install.sh | bash
nvm install 22.22.2
nvm use 22.22.2

Permission errors:

# Fix npm permissions
mkdir ~/.npm-global
npm config set prefix '~/.npm-global'
echo 'export PATH=~/.npm-global/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

Tool Installation Issues

samtools not found:

# Check if installed
which samtools

# Add to PATH if needed
echo 'export PATH=/usr/local/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

Version too old:

# Remove old version
sudo apt remove samtools

# Install from source or use conda
conda install -c bioconda samtools=1.17

Package Installation Issues

NPM installation fails:

# Clear npm cache
npm cache clean --force

# Remove node_modules and reinstall
rm -rf node_modules package-lock.json
npm install

Network/proxy issues:

# Configure npm proxy (if needed)
npm config set proxy http://proxy.company.com:8080
npm config set https-proxy http://proxy.company.com:8080

Platform-Specific Notes

Windows

• WSL Recommended: Use Windows Subsystem for Linux for best compatibility
• Native Windows: PowerShell or Command Prompt work, but some features may be limited
• Path Separators: Use forward slashes / in file paths even on Windows

macOS

• Xcode Tools: May need xcode-select --install for some dependencies
• M1/M2 Macs: All tools are compatible with Apple Silicon
• Homebrew: Recommended package manager for bioinformatics tools

Linux

• Distribution: Tested on Ubuntu 20.04+, CentOS 7+, and Debian 10+
• Permissions: Some distributions require sudo for global installations
• SELinux: May need to configure SELinux policies in enterprise environments

Next Steps

After successful installation:

1. Configuration - Set up your environment
2. Getting Started - Run your first download
3. Authentication - Configure secure access

Updates

To update to the latest version:

cd varvis-download
git pull origin main
npm install

Check for new releases at: https://github.com/LaborBerlin/varvis-download/releases