Installation
moments
now supports Python 3. Because Python is soon discontinuing support for
Python 2, we do not actively ensure that moments remains fully compatable with Python
2, and strongly recommend using Python 3.
Using conda
moments
is available via Bioconda.
The most recent release of moments
can be installed by running
conda install -c bioconda moments
The conda channels must be set up to include bioconda, which can be done by running
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Using pip
A simple way to install moments
is via pip
. numpy
, mpmath
, and cython
are install requirements, but installing moments
directly from the git repository
using pip
should install these dependencies automatically:
pip install git+https://bitbucket.org/simongravel/moments.git
This approach can also be used to install the development branch of moments
:
pip install git+https://bitbucket.org/simongravel/moments.git@devel
Alternatively, you can clone the git repository
git clone https://bitbucket.org/simongravel/moments.git
and then from within the moments directory (cd moments
), run
pip install -r requirements.txt
pip install .
Dependencies and details
moments
and moments.LD
requires a number of dependencies. Minimally,
these include
numpy
scipy
cython
mpmath
demes
All dependencies are listed in requirements.txt, and can be install together using
pip install -r requirements.txt
We also strongly recommend installing ipython
for interactive analyses.
If you are using conda, all dependencies can be installed by navigating to the moments directory and then running
conda install --file requirements.txt
Once dependencies are installed, to install moments
, run the following commands
in the moments directory:
python setup.py build_ext --inplace
python setup.py install
or
pip install .
Note that you might need sudo privileges to install in this way.
You should then be able to import moments
in your python scripts. Entering an
ipython or python session, type import moments
. If, for any reason, you have
trouble installing moments
after following these steps, please submit an
Issue.
If you use Parsing
from moments.LD
, which reads VCF-formatted files and
computes LD statistics to compare to predictions from moments.LD
, you will need to
additionally install
hdf5
scikit-allel