Installation

Installation should take less than 5 minutes.

System Requirements

CentOS Linux 7 or above

Required packages

Package management

conda >24.7.1 or above

Download here: https://github.com/conda-forge/miniforge

or for running software in containers

apptainer

Download here: https://apptainer.org/docs/user/latest/quick_start.html#installation

Workflow language

snakemake 8.24.1 or above

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

Clone repository

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

Set up snakemake environment with conda

This pipeline uses python2.7 and python ≥3.7 with additional R scripts in a Snakemake pipeline. The .yml files provided will create the appropriate environments and is completely handled by MPRAsnakeflow. 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 MPRAsnakeflow
conda create -c conda-forge -c bioconda -n snakemake snakemake

# activate snakemake
conda activate snakemake

To deactivate the environment, use:

conda deactivate

Quick test

conda activate snakemake
snakemake --help