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/and moments (>= 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.

Auto mode

One could install everything with install script:

$ ./install

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
    
  1. 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!