Installation¶
Note
Wheels are provided for Linux, OSX and Windows x86-64, as well
as Linx Aarch64, but other machines will have to build the wheel from the
source distribution. Building pytrimal
involves compiling trimAl,
which requires a C++ compiler to be available on the local machine.
PyPi¶
pytrimal
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 pytrimal
either from a wheel if
one is available, or from source after compiling the Cython code :
$ pip install --user pytrimal
Conda¶
pytrimal
is also available as a recipe
in the bioconda channel. To install, simply
use the conda
installer:
$ conda install -c bioconda pytrimal
Arch User Repository¶
A package recipe for Arch Linux can be found in the Arch User Repository under the name python-pytrimal. 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-pytrimal
Piwheels¶
PytrimAl works on Raspberry Pi platforms (with NEON vectorization enabled!), and
pre-built wheels are made available for armv7l
platforms. Run the following
command to install them instead of compiling from source:
$ pip3 install pytrimal --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):
$ git clone --recursive https://github.com/althonos/pytrimal
$ pip install --user ./pytrimal
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/pytrimal
$ cd pytrimal
$ 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.