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.

Installing an unreleased development version

If you for some reason want to use the most recent development version of WhatsHap, you can install it in the following way. These instructions will create a virtual environment in the directory whatshap-env that contains WhatsHap. Simply delete that directory to uninstall the software. Other WhatsHap versions you may have installed in other locations remain unaffected.

python3 -m venv whatshap-env
whatshap-env/bin/pip install Cython
whatshap-env/bin/pip install git+

You can then run WhatsHap like this:

whatshap-env/bin/whatshap --version

You should see a version number like 0.17+103.g71e5b3c, which means that this version is 103 Git commits ahead of version 0.17.