Skip to content
bredelingsPublic

About

Bayesian co-estimation of phylogenies and multiple alignments via MCMC

Resources

Contributing

Stars

50 stars

Watchers

2 watching

Forks

Repository files navigation

Build and test

Install

If you just want to install bali-phy, please visit the release page. If you want to compile BAli-phy from source, the quick-start instructions are below.

Compiling

You will need a C++ compiler that understands C++23.

The oldest compiler versions tested in CI are:

  • GCC 13
  • Clang 18
  • Xcode 16

Install Prerequisites

On Ubuntu 24.04 (or higher), or on Debian testing, you can use apt-get:

sudo apt-get install g++ libcairo2-dev meson libboost-all-dev libcli11-dev pandoc

On Mac (or Linux, actually) you can use homebrew:

brew install cairo meson boost cli11

On miniconda, you can use:

conda create -n devel -c conda-forge --strict-channel-priority
conda activate devel
conda install meson gxx boost-cpp cmake pkg-config cairo
export BOOST_ROOT=$CONDA_PREFIX

Meson version

After installing prerequisites above, check that the Meson version is at least 1.6.

meson --version

If your version of Meson is less than 1.6, install a newer version into a Python virtual environment:

python3 -m venv meson_venv
source meson_venv/bin/activate
pip install meson ninja

Build BAli-Phy

This will build the latest version of BAli-Phy. It may have some changes that have not yet been released. Check the [NEWS.md] file for the details.

git clone https://github.com/bredelings/BAli-Phy.git
cd BAli-Phy
meson setup build --prefix=$HOME/Applications/bali-phy
ninja -C build install
ninja -C build test

Adding bali-phy to your $PATH

In order to run the installed software, you should add bali-phy to your $PATH.

Installed locations

If you installed in $HOME/Applications/bali-phy/ as recommended above, then files will be in:

Location Files
~/Applications/bali-phy/bin Binary executables.
~/Applications/bali-phy/share/bali-phy/examples/ Example files.
~/Applications/bali-phy/share/doc/bali-phy/ Documentation.

Further Documentation

The Manual describes how to install bali-phy in greater detail.

About

Bayesian co-estimation of phylogenies and multiple alignments via MCMC

Resources

Contributing

Stars

50 stars

Watchers

2 watching

Forks

Releases

Packages

Used by

Contributors

Languages