Installation

Prerequisites

git and a conda distribution (e.g. Miniconda or Miniforge) must be installed first.

git clone https://github.com/MicrobiologyETHZ/satay_tools.git
cd satay_tools
conda env create -f satay_environment.yaml
conda activate satay-tools
pip install --no-deps .

satay --help

Note

The align step requires Linux. It runs the STAR aligner, which does not work on macOS (STAR fails to read the input reads). Run align on a Linux machine. The other steps (map, merge and analyze) work on both macOS and Linux.