Installation¶
Note
Wheels are provided for Linux and OSX x86-64 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.
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
Conda¶
Pronto is also available as a recipe
in the bioconda channel. To install, simply
use the conda
installer:
$ conda install -c bioconda pyhmmer
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 --user https://github.com/althonos/pyhmmer/archive/master.zip
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.