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.
pyhmmer involves compiling HMMER3 and Easel, which requires a
C compiler to be available.
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.
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
$ 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
yay, etc.). For
aura, you’ll need to run:
$ aura -A python-pyhmmer
PyHMMER works on Raspberry Pi computers (with NEON vectorization enabled),
and pre-built wheels are compiled for
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.
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
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.
If you do not want to use
pip, you can still clone the repository and
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
Installing packages without
pip is strongly discouraged, as they can
only be uninstalled manually, and may damage your system.