README.md

sksurv-bio-workflows

Installation

Install and set up Mambaforge

Clone git repository and submodules:

git clone [email protected]:hermidalc/sksurv-bio-workflows.git
cd sksurv-bio-workflows
git submodule update --init --recursive

To install conda environment on Intel architecture hardware:

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

Otherwise:

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

Activate the environment:

mamba activate sksurv-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/sksurv-bio-workflows-mkl.yml

Otherwise:

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