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, but we recommend using the Windows Subsystem for Linux (WSL) for the best experience. If you are using WSL, please follow the instructions for Linux.

GADMA is available for MacOS system.

Activate Conda Environment

conda activate gadma_workshop_env

Installation

  • Install specified version of moments (unfortunately, GADMA is not yet compatible with the most recent version):

    pip install moments-popgen==1.3.1

  • 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

We will use a specific version of matplotlib to avoid some warnings:

pip install "matplotlib<3.5"

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 | xargs

  • 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.