Installation
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.
Note
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+https://github.com/whatshap/whatshap
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
.