GADMA Installation

During the workshop you will learn how to use GADMA for demographic inference. We kindly ask you to install GADMA on your system using the instructions below.

Platform

Choose your platform to get recommendations and installation instructions:

GADMA is available for Linux system.

GADMA is available for Windows system.

GADMA is available for MacOS system.

Set Up Conda Environment

We recommend to create and set up an empty conda environment:

$ conda create -n gadma_env python=3.10
$ conda activate gadma_env

Add channels that we are going to use for installation:

$ conda config --add channels bioconda
$ conda config --add channels conda-forge

Installation

  • Install GADMA using pip:

    $ pip install gadma

  • Install GADMA using pip:

    $ pip install gadma

  • Install dadi and scikit-allel using conda first:

    $ conda install dadi scikit-allel

  • Install GADMA using pip:

    $ pip install gadma

Check the version of matplotlib

In order to successfully draw models, GADMA requires matploltib package no higher than 3.7.5. Check that the correct varsion is installed:

$ pip install "matplotlib<=3.7.5"

Verify Installation

  1. To verify installation first run:

    $ gadma --test

    You should see the following output:

    --Finish pipeline--

--Test passed correctly--

Thank you for using GADMA!

In case of any questions or problems, please contact: ekaterina.e.noskova@gmail.com

  2. Download example data example_input_for_gadma.sfs and input file gadma_params.sfs:

    $ wget https://github.com/noscode/GADMA_workshops/raw/refs/heads/main/docs/source/2024_18_11/files/example_input_for_gadma.sfs
$ wget https://github.com/noscode/GADMA_workshops/raw/refs/heads/main/docs/source/2024_18_11/files/gadma_params

    And run:

    $ gadma -p gadma_params

    You should see the following output:

    --Finish pipeline--

Let Us Know You Were Successful

In order for us to understand how many participants are ready for the workshop, we ask you to send us some results of your run.

  • Print the following line of the file gadma_output/GADMA.log:

    $ tail -25 gadma_output/GADMA.log | head -1

  • Please send us this line via the following form:

Send Your Result

Troubleshooting

If you have any problems with installation:

  • You can install GADMA using conda

    $ conda install gadma

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

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

    Run GADMA installation after.

  • Take a look at the official installation documentation

  • If you still face issues, please write to ekaterina.e.noskova@gmail.com.