Installation

Caution

Windows is not supported by HMMER, so it is not possible to build PyHMMER on Windows as the moment. Consider using a Python install inside the Windows Subsystem for Linux if you need PyHMMER on a Windows computer.

PyPi

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

$ pip install --user pyhmmer

Note

Wheels are provided for Linux and MacOS on x86-64 and NEON-enabled Arm platforms, but other machines will have to build the wheel from the source distribution. Building pyhmmer involves compiling HMMER3 and Easel, which requires a C compiler to be available.

Conda

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

$ conda install -c bioconda pyhmmer

Arch User Repository

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

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 -Sy
$ pacman -S python-pyhmmer

Piwheels

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

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

Check the piwheels documentation 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):

$ pip install -U git+https://github.com/althonos/pyhmmer

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/pyhmmer
$ cd pyhmmer
$ python setup.py build
# python setup.py install

Danger

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