Installation

Note

Wheels are provided for Linux, MacOS and Windows x86-64, as well as Linux and MacOS Aarch64, but other machines will have to build the wheel from the source distribution. Building pyrodigal involves compiling Prodigal, which requires a C compiler to be available.

PyPi

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

$ pip install --user pyrodigal

Conda

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

$ conda install -c bioconda pyrodigal

Arch User Repository

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

BioArchLinux

The BioArchLinux project provides pre-compiled packages based on the AUR recipe. Add the BioArchLinux package repository to /etc/pacman.conf:

[bioarchlinux]
Server = https://repo.bioarchlinux.org/$arch

Then install the latest version of the package and its dependencies with pacman:

$ pacman -S python-pyrodigal

Piwheels

Pyrodigal works on Raspberry Pi computers (with NEON vectorization enabled!), and pre-built wheels are compiled for armv7l platforms on piwheels. Run the following command to install these instead of compiling from source:

$ pip3 install pyrodigal --extra-index-url https://www.piwheels.org/simple

Check the piwheels documentation for more information.

FreeBSD Port

On BSD systems, Pyrodigal is available as a port and can be installed as a compiled package with one of the following commands:

$ pkg install biology/py-pyrodigal
$ pkg install py39-pyrodigal

See the FreshPorts page for more information.

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/pyrodigal
$ pip install --user ./pyrodigal

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/pyrodigal
$ cd pyrodigal
$ 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.