Installation

Set up conda environment

In order to avoid issues, we recommend to create an empty conda environment. The current version of GADMA (greater than 2.0.0) supports Python3 only. .. code-block:: console

$ conda create -n gadma_env python=3.10 $ conda activate gadma_env $ conda config –add channels bioconda $ conda config –add channels conda-forge

Installing the latest release

The latest release of GADMA can be easily installed via pip or conda (bioconda):

$ pip install gadma

or

$ conda install -c bioconda gadma

This will install GADMA with dadi, moments and momentsLD engines.

Warning

Sometimes some dependencies (e.g. dadi or scikit-allel) fail to install when GADMA is installed using pip. You can install them using conda before the installation of GADMA:

$ conda install dadi scikit-allel

If you faced an issue for moments (moments-popgen) package on MacOS, try installing it independently using:

$ pip install Cython
$ pip install "setuptools_scm>=8"
$ pip install --no-build-isolation moments-popgen

If you want to use momi2 engine, please install it:

$ pip install momi

Note

momi package sometimes is not installed correctly for Windows and MacOS. If momi is not available please install it manually following the installation instructions in momi’s manual.

Verifying installation

To verify the installation, run:

$ 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!

Dependencies

Below we hightlight GADMA dependencies:

  • Python3

  • numPy

  • scipy

  • matplotlib

  • Pillow (>= 4.2.1)

  • pandas (<= 2.2.2)

  • ruamel.yaml (== 0.16.12)

  • dadi

  • moments

  • momi

  • moments.LD (is installed alongside with moments)

  • h5py == 3.10.0 (for momentsLD)

  • scikit-allel (for moments)

If you wish to use moments for demographic models plotting you need older version of matplotlib:

To calculate confidence intervals one should install (requirements/minimal.txt):

  • pandas

To run Bayesian optimization smac of specified version is requered (requirements/bayes_opt.txt):

  • scikit-optimize

  • configspace

  • bayesmark

  • smac (==0.13.1)

Troubleshooting

If there are some troubles installing the engine, please, first of all check the table below for the ability to install this engine on your system. You are always welcome to open an issue on GitHub for getting help.

GADMA has automatic tests on GitHUb for engines on different systems (Linux, Windows, MacOS). The following table indicates (according to our tests) if engine could be installed on specified system:

Feature

dadi

moments

momi

momentsLD

Linux

✅

✅

✅

✅

Windows

✅

✅

❌

✅

MacOS

✅

✅

✅

✅

Manual installation

Some features are added to the GADMA project but are not released yet. One can install GADMA directly from the repository.

First clone the repository:

$ git clone https://github.com/ctlab/GADMA.git
$ cd GADMA

Run installation:

$ pip install .