Installation (Linux & MacOS)

Installation

This page describes how to install STOAT and its dependencies on Linux and macOS.

Dependencies

Linux

On Debian/Ubuntu-based systems, install the required dependencies with:

sudo apt-get update
sudo apt-get install build-essential cmake pkg-config \
    libjansson-dev protobuf-compiler libprotoc-dev libprotobuf-dev \
    libboost-all-dev libhts-dev valgrind

macOS [intel chips]

STOAT uses Homebrew for some of its dependencies.

Install the required Homebrew packages:

brew install libomp htslib boost pkg-config

Protobuf

STOAT requires Protobuf v29.0. Install it locally with:

cd ~/local

git clone --branch v29.0 https://github.com/protocolbuffers/protobuf.git
cd protobuf

git submodule update --init --recursive

cmake -S . -B build \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_CXX_STANDARD=17 \
    -DCMAKE_CXX_STANDARD_REQUIRED=ON \
    -DCMAKE_CXX_EXTENSIONS=OFF \
    -Dprotobuf_BUILD_TESTS=OFF \
    -DCMAKE_INSTALL_PREFIX="$HOME/local/protobuf"

cmake --build build --parallel
cmake --install build

Jansson

STOAT requires Jansson v2.14. Install it locally with:

cd ~/local

git clone --branch v2.14 https://github.com/akheron/jansson.git
cd jansson

cmake -S . -B build \
    -DCMAKE_BUILD_TYPE=Release \
    -DCMAKE_INSTALL_PREFIX="$HOME/local/jansson" \
    -DJANSSON_BUILD_DOCS=OFF \
    -DJANSSON_BUILD_TESTS=OFF

cmake --build build --parallel
cmake --install build

Environment variables

Add the locally installed libraries and Homebrew dependencies to the environment:

export PKG_CONFIG_PATH="$HOME/local/jansson/lib/pkgconfig:$(brew --prefix htslib)/lib/pkgconfig:$PKG_CONFIG_PATH"

export CMAKE_PREFIX_PATH="$HOME/local/protobuf:$HOME/local/jansson:$(brew --prefix htslib):$(brew --prefix boost):$CMAKE_PREFIX_PATH"

These variables must be set before configuring STOAT.

Optional dependencies

• vg — optional

STOAT uses libbdsg and libvgio, both of which depend on libhandlegraph.

STOAT uses its own copies of these libraries. However, if compatible libraries are already installed on your system, version conflicts may occur. In general, the latest versions of these tools should work.

Docker

STOAT can also be built and run using Docker.

• Dockerfile
• Docker image on Quay.io: quay.io/patou/stoat

Build

Clone the repository with its submodules:

git clone --recursive https://github.com/Pa-Tou/stoat.git
cd stoat

Configure and build STOAT:

cmake -S . -B build
cmake --build build --parallel

The stoat binary will be created in stoat/bin.

From the main STOAT directory, run:

./bin/stoat

Note: STOAT currently uses dynamic compilation on both Linux and macOS.