Configuration

Example dataset#

You can test GenoML on an example dataset. To install the examples/ directory (~315 KB), you can use SVN (pre-installed on most Macs):

svn export https://github.com/GenoML/genoml2.git/trunk/examples

tip

When you pip install this package, the examples/ folder is also downloaded! However, if you still want to download the directory and SVN is not pre-installed, you can download it via Homebrew if you have that installed using brew install svn.

[OPTIONAL] Setting up a virtual environment via Conda#

You can create a virtual environment to run GenoML, if you prefer. If you already have the Anaconda Distribution, this is fairly simple.

To create and activate a virtual environment:

# To create a virtual environment
conda create -n GenoML python=3.7

# To activate a virtual environment
conda activate GenoML

# To install requirements via pip 
pip install -r requirements.txt
    # If issues installing xgboost from requirements - (3 options)
        # use Homebrew to 
            # xcode-select --install
            # brew install gcc@7
        # conda install -c conda-forge xgboost 
        # pip install xgboost==0.90

## MISC
# To deactivate the virtual environment
# conda deactivate GenoML

# To delete your virtual environment
# conda env remove -n GenoML

To install the GenoML in the user's path in a virtual environment, you can do the following:

# Install the package at this path
pip install .

# MISC
    # To save out the environment requirements to a .txt file
# pip freeze > requirements.txt

    # Removing a conda virtualenv
# conda remove --name GenoML --all 