Installation

Installation should take less than 5 minutes

System Requirements

CentOS Linux 7 or above

Required packages

conda >24.7.1

Download here: https://docs.conda.io/en/latest/miniconda.html

snakemake 8.27.1 or above

Download here: https://snakemake.readthedocs.io/

Clone repository

Download here: https://github.com/kircherlab/MPRAOligoDesign.git

Set up conda with snakemake environment

The whole pipeline is set up to run on a Linux system.

Install the the conda environment. The general conda environment is called snakemake.

cd MPRAOligoDesign
conda create -c bioconda -c conda-forge -n snakemake snakemake

# activate snakemake
conda activate snakemake

To deactivate the environment, use:

conda deactivate

Quick test

conda activate snakemake
snakemake --help