Installation¶
Dependencies¶
Current version of GADMA (later than 2.0.0) supports Python3 only. Older versions supported Python 2 as well but not any more.
GADMA requires the following dependencies:
Python3
NumPy (>= 1.2.0)
Scipy (>= 0.6.0)
ruamel.yaml
dadi
(>= 1.7.0) or/andmoments
(>= 1.0.0)nlopt (for
dadi
)Cython (for
moments
)mpmath (for
moments
)
To draw demographic models one should install the following:
matplotlib (>= 0.98.1)
Pillow (>= 4.2.1) - optional
moments
(>= 1.0.0)
To calculate Confidence Intervals:
pandas
Installing the latest release¶
The latest release of BoTorch is easily installed either via pip
:
$ pip install gadma
Warning
Installation via pip
will not install moments
library. To install it one should run:
$ pip install --upgrade Cython
$ pip install mpmath
$ git clone https://bitbucket.org/simongravel/moments/
$ cd moments
$ python3 setup.py install
$ cd ..
Manual installation¶
Some features are added to GADMA project but are not released yet. One can try to install GADMA directly from the repository.
First clone repository:
$ git clone https://github.com/ctlab/GADMA.git $ cd GADMA
Dependencies could be installed with one of two modes.
Full-manual mode¶
Install dependencies manually:
- NumPy
$ pip install numpy
- Scipy
$ pip install scipy
- ruamel.yaml
$ pip install ruamel.yaml
dadi
, nlopt$ pip install dadi
moments
, mpmath, Cython $ pip install --upgrade Cython $ pip install mpmath $ git clone https://bitbucket.org/simongravel/moments/ $ cd moments $ python3 setup.py install $ cd ..
- matplotlib
$ pip install matplotlib
- Pillow
$ pip install Pillow
- pandas
$ pip install pandas
- Install GADMA
$ python3 setup.py install
Verifying installation¶
To verify the installation, run a test:
$ gadma --test
If the installation was successful, one will find the following information at the end:
--Finish pipeline--
--Test passed correctly--
Thank you for using GADMA!