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 pyfamsa involves compiling FAMSA, which requires a C++ compiler to be available on the local machine.

PyPi

pyfamsa 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 pyfamsa either from a wheel if one is available, or from source after compiling the Cython code :

$ pip install --user pyfamsa

Conda

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

$ conda install -c bioconda pyfamsa

Arch User Repository

A package recipe for Arch Linux can be found in the Arch User Repository under the name python-pyfamsa. 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-pyfamsa

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 --recursive https://github.com/althonos/pyfamsa
$ pip install --user ./pyfamsa

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 + setuptools

If you do not want to use pip, you can still clone the repository and run the setup.py file manually, although you will need to install the build dependencies (mainly Cython):

$ git clone --recursive https://github.com/althonos/pyfamsa
$ cd pyfamsa
$ python setup.py build_ext
# python setup.py install

Danger

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