Installation

Requirements

The current validated environment is:

• Linux

• conda-based Python environment

• Python 3.12

The main tutorial and recommended workflow are currently oriented toward this environment.

Install from PyPI

The recommended way to install SMODER is:

pip install smoder

Install from GitHub

To install the latest development version from source:

git clone https://github.com/HokazeJunko/SMODER.git
cd SMODER
pip install -e .

Create a Python environment

For example:

conda create -n smoder python=3.12
conda activate smoder

Current recommended execution method

python -m smoder.pipelines.mousebrain_h3k27ac

Data preparation

Before running the example workflow, please prepare the required input files as described in the Data page.