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

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
# 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 .
# To save out the environment requirements to a .txt file
# pip freeze > requirements.txt
# Removing a conda virtualenv
# conda remove --name GenoML --all