hermidalc/sklearn-bio-workflows

Framework to build, evaluate, select, and compare ML classification and regression models using high-dimensional biological data and other covariates

sklearn-bio-workflows

Installation

Install and set up Miniforge3

Clone git repository and submodules:

git clone --recurse-submodules https://github.com/hermidalc/sklearn-bio-workflows.git
cd sklearn-bio-workflows

To install conda environment on Intel architecture hardware:

mamba env create -f envs/sklearn-bio-workflows-mkl.yml

Otherwise:

mamba env create -f envs/sklearn-bio-workflows.yml

Activate the environment:

mamba activate sklearn-bio-workflows

Install non-conda packages into environment:

./utils/install_nonconda_r_pkgs.R

Updates

Update the git repository and submodules:

git pull
git submodule update --recursive

To update the conda environment on Intel architecture hardware:

mamba env update -f envs/sklearn-bio-workflows-mkl.yml

Otherwise:

mamba env update -f envs/sklearn-bio-workflows.yml