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Installation#

This guide covers all the ways to install the oxo-flow binary on your system.

Requirements#

  • Operating system: Linux (x86_64, aarch64) or macOS (Apple Silicon, Intel)
  • Disk space: ~50 MB for the binary
  • Optional: Rust toolchain (1.85+) if building from source

Runtime dependencies

oxo-flow itself has no runtime dependencies — it is a single static binary. However, the tools your workflows call (e.g., bwa, samtools, GATK) must be available either on your $PATH or through an environment manager (conda, docker, etc.) declared in your .oxoflow file.

If you have the Rust toolchain installed:

cargo install oxo-flow

This builds the latest published release and places the oxo-flow binary in ~/.cargo/bin/.

Verify the installation:

oxo-flow --version
# oxo-flow 0.1.0

Updating

Run the same cargo install oxo-flow command to update to the latest version. Cargo will rebuild if a newer version is available.

Option 2 — Build from Source#

Clone the repository and build the workspace:

git clone https://github.com/Traitome/oxo-flow.git
cd oxo-flow
cargo build --release

The binary is at target/release/oxo-flow. Copy it to a directory on your $PATH:

cp target/release/oxo-flow ~/.local/bin/

Development build#

For faster compile times during development (without optimizations):

cargo build
# Binary at: target/debug/oxo-flow

Option 3 — Download Pre-built Binary#

Pre-built binaries are available from the GitHub Releases page.

# Example for Linux x86_64
curl -LO https://github.com/Traitome/oxo-flow/releases/latest/download/oxo-flow-linux-x86_64.tar.gz
tar xzf oxo-flow-linux-x86_64.tar.gz
chmod +x oxo-flow
mv oxo-flow ~/.local/bin/

Shell Completions#

oxo-flow can generate shell completions for Bash, Zsh, Fish, Elvish, and PowerShell:

oxo-flow completions bash > ~/.local/share/bash-completion/completions/oxo-flow

oxo-flow completions zsh > ~/.zfunc/_oxo-flow
# Add to .zshrc: fpath+=~/.zfunc && autoload -Uz compinit && compinit

oxo-flow completions fish > ~/.config/fish/completions/oxo-flow.fish

Verify Installation#

After installation, confirm everything is working:

# Check version
oxo-flow --version

# Show help
oxo-flow --help

# Initialize a test project
oxo-flow init my-test-pipeline
cd my-test-pipeline
oxo-flow validate my-test-pipeline.oxoflow

Expected output:

✓ my-test-pipeline.oxoflow — 0 rules, 0 dependencies

Next Steps#