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
python3-dev will take care of all required
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.