Installation of WhatsHap is easiest if you use Conda.

Installation with Conda

First, ensure you have Conda (miniconda or Anaconda) installed and made the proper settings to enable the “bioconda” channel. For that, follow the bioconda installation instructions.

Then WhatsHap can be installed with this command:

conda install whatshap

If you have Conda, but not enabled bioconda, use this command:

conda install -c bioconda -c conda-forge whatshap

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 3.3 (or later) and the corresponding Python header files. Python 3.5 is slightly faster than 3.4. 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.