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
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+https://github.com/whatshap/whatshap
Then check whether you are using the development:
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
To get rid of the development installation, just run
conda env remove -n whatshap-tmp.