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Installation

The haddock-runner is designed for researchers, developers, and advanced users who are familiar with HADDOCK and command-line computing. It is particularly suited for those with access to HPC infrastructure for running large-scale docking experiments.

Prerequisites

HADDOCK3 Installation

IMPORTANT: haddock-runner requires HADDOCK3 to be installed on your system.

This tool is not a replacement for HADDOCK itself, but rather a benchmarking framework that automates the execution of multiple HADDOCK runs.

If you are new to HADDOCK, we recommend:

  • Completing the basic HADDOCK3 tutorials
  • Familiarizing yourself with HADDOCK3 workflows and configuration

For single target docking or small-scale experiments, consider using:

System Requirements

  • Operating System: Linux (recommended), macOS, or Windows with WSL
  • Memory: Minimum 8GB RAM (16GB+ recommended for concurrent execution)
  • Storage: Sufficient disk space for input structures and results
  • HPC Access: Recommended for large-scale benchmarks

Installation Methods

The easiest way to install haddock-runner is through cargo, Rust’s package manager:

# Install directly from crates.io
cargo install haddock-runner

# This will install the binary to ~/.cargo/bin/haddock-runner

Note: If you don’t have cargo installed, you can install Rust from https://www.rust-lang.org/tools/install

After installation, ensure the cargo bin directory is in your PATH:

# Add cargo bin to your PATH (add this to your ~/.bashrc or ~/.zshrc)
export PATH="$HOME/.cargo/bin:$PATH"

# Verify installation
source $HOME/.cargo/env
haddock-runner --version

Method 2: Install Pre-built Binary from GitHub Releases (Coming Soon)

Pre-compiled binaries will be available for each release on GitHub:

# Download the latest release for your platform
# Check https://github.com/haddocking/haddock-runner/releases for the latest version
VERSION="v3.0.0"  # Update to latest version
OS_ARCH="x86_64-unknown-linux-gnu"  # Choose your platform

wget https://github.com/haddocking/haddock-runner/releases/download/${VERSION}/haddock-runner-${OS_ARCH}

# Make it executable
chmod +x haddock-runner-${OS_ARCH}

# Move to your PATH (optional)
sudo mv haddock-runner-${OS_ARCH} /usr/local/bin/haddock-runner

# Verify installation
haddock-runner --version

Available platforms will include:

  • x86_64-unknown-linux-gnu (Linux 64-bit)
  • x86_64-apple-darwin (macOS Intel)
  • aarch64-apple-darwin (macOS Apple Silicon)

Note: Pre-built binaries are coming soon. For now, please use Method 1 (crates.io) or see the Development section for building from source.

Post-Installation Setup

Add to PATH (Optional)

To make haddock-runner available system-wide:

# Create a symlink or copy the binary to a directory in your PATH
sudo ln -s $(pwd)/target/release/haddock-runner /usr/local/bin/haddock-runner

# Verify it's accessible
which haddock-runner
haddock-runner --version

Verify HADDOCK3 Integration

Before running benchmarks, ensure HADDOCK3 is properly installed and accessible:

# Check HADDOCK3 installation
haddock3 --version

# Verify required modules are available
haddock3 --list-modules

Troubleshooting

Common Issues

Rust installation problems:

  • Ensure you have proper internet connectivity
  • Check that you have required system dependencies (build-essential, curl, etc.)
  • Try rustup update if you already have Rust installed

Missing HADDOCK3:

  • Ensure HADDOCK3 is installed and in your PATH
  • Check that all required HADDOCK modules are available
  • Verify your HADDOCK3 configuration files are properly set up

Permission issues:

  • Ensure you have read/write access to the working directory
  • Check that input files are readable
  • Verify you have execution permissions for the binary

Getting Help

If you encounter installation issues:

Next Steps

Now that you have haddock-runner installed, you’re ready to:

  1. Set up your first benchmark - See Setting Up a Benchmark
  2. Write a configuration file - See Writing a Benchmark YAML File
  3. Prepare your input files - See Writing an Input List File
  4. Run your benchmark - See Running Haddock Runner