Installation

Note

Wheels are provided for Linux and OSX x86-64, but other machines will have to build the wheel from the source distribution. Building pyskani involves compiling skani, which requires a Rust compiler to be available on the local machine.

PyPi

pyskani is hosted on GitHub, but the easiest way to install it is to download the latest release from its PyPi repository. It will install all dependencies then install pyskani either from a wheel if one is available, or from source after compiling the Cython code :

$ pip install --user pyskani

Conda

pyskani is also available as a recipe in the bioconda channel. To install, simply use the conda installer:

$ conda install -c bioconda pyskani

Arch User Repository

A package recipe for Arch Linux can be found in the Arch User Repository under the name python-pyskani. It will always match the latest release from PyPI.

Steps to install on ArchLinux depend on your AUR helper (yaourt, aura, yay, etc.). For aura, you’ll need to run:

$ aura -A python-pyskani

GitHub + pip

If, for any reason, you prefer to download the library from GitHub, you can clone the repository and install the repository by running (with the admin rights):

$ git clone https://github.com/althonos/pyskani
$ pip install --user ./pyskani

Caution

Keep in mind this will install always try to install the latest commit, which may not even build, so consider using a versioned release instead.

GitHub + build

If you do not want to use pip, you can still clone the repository and use build and installer manually:

$ git clone --recursive https://github.com/althonos/pyskani
$ cd pyskani
$ python -m build .
# python -m installer dist/*.whl

Danger

Installing packages without pip is strongly discouraged, as they can only be uninstalled manually, and may damage your system.