Installation of WhatsHap is easiest if you use Conda.

Installation with Conda

First, follow the Bioconda installation instructions.

Make sure you configured the bioconda and conda-forge channels as stated in those instructions. Even if you have previously set up those channels, you can repeat the conda config add --channels ... commands to ensure your configuration is correct.


It is not sufficient to only add -c bioconda to the conda create or conda install commands as both the bioconda and the conda-forge channels are required and must be listed in the correct order. Refer to the Bioconda instructions for using command-line options instead of modifying the Conda configuration.

Then install WhatsHap into a new Conda environment (here named whatshap-env):

conda create -n whatshap-env whatshap

Then activate the environment. Whenever you start a new shell and want to use WhatsHap, you need to repeat this step:

conda activate whatshap-env

Finally, check whether you got the most recent WhatsHap version:

whatshap --version

The most recent version is listed at the top of the changelog.

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.