Installation of WhatsHap is easiest if you use Conda.

Installation with Conda

If you do not have Conda, follow the the Bioconda installation instructions.

If you already have Conda (for example, miniconda or Anaconda) installed, ensure you have enabled both the “bioconda” and “conda-forge” channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Then WhatsHap can be installed with this command:

conda install whatshap

For a smaller download and installation size, add nomkl to this command. This will avoid installing the (quite large) “Intel Math Kernel Library”, which WhatsHap does not use anyway:

conda install whatshap nomkl

Installation with pip

Before you can pip install, you need to install dependencies that pip cannot install for you. WhatsHap is implemented in C++ and Python. You need to have a C++ compiler, Python 3.7 or later and the corresponding Python header files. In Ubuntu, installing the packages build-essential and python3-dev will take care of all required dependencies.

WhatsHap can then be installed with pip:

pip3 install --user whatshap

This installs WhatsHap into $HOME/.local/bin. Then add $HOME/.local/bin to your $PATH and run the tool:

export PATH=$HOME/.local/bin:$PATH
whatshap --help

Alternatively, you can also install WhatsHap into a virtual environment if you are familiar with that.

Installing an unreleased development version

If you want to use the most recent development version of WhatsHap, you can install it in the following way into a separate Conda environment. This way, other WhatsHap versions you may have installed in other locations remain unaffected. Make sure you have installed Conda. Then run:

conda create -n whatshap-tmp python pip gxx
conda activate whatshap-tmp
pip install git+

Then check whether you are using the development:

whatshap --version

You should see a version number like 0.18.dev119+g5ba23de, which means that this is going to become version 0.18, with 119 commits ahead of the previous version (0.17).

To get rid of the development installation, just run conda env remove -n whatshap-tmp.