Installation Guide

This guide will help you install and set up the S2-omics package.

Installation

For convenience, we recommend creating and activating a dedicated conda environment before installing S2-omics. If you haven’t installed conda yet, we suggest using Miniconda, a lightweight distribution of conda.

# We recommand using Python 3.11 or above
conda create -n s2omics python=3.11
conda activate s2omics

The S2-omics package can be downloaded by:

# download S2-omics package
git clone https://github.com/ddb-qiwang/S2Omics
cd S2Omics

The cosie_env environment can be used in Jupyter Notebook by:

pip install ipykernel
python -m ipykernel install --user --name s2omics --display-name s2omics

Dependencies

All other required packages are listed in requirements.txt. You can install them by running:

pip install -r requirements.txt
# if your server has a very old version of GCC, you can try: pip install -r requirements_old_gcc.txt