Installation

Installation should take less than 5 minutes.

System Requirements

CentOS Linux 7 or above

Required Packages

Package Management

You will need either conda or apptainer for managing dependencies:

Conda (version ≥ 24.7.1)
```
conda >24.7.1
```
Download here: https://github.com/conda-forge/miniforge
Apptainer (for running software in containers)
```
apptainer
```
Download here: https://apptainer.org/docs/user/latest/quick_start.html#installation

Workflow Language

You will also need snakemake (version ≥ 8.24.1):

snakemake 8.24.1

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

Clone Repository

Clone the MPRAsnakeflow repository from GitHub:

git clone https://github.com/kircherlab/MPRAsnakeflow.git

Set Up Snakemake Environment with Conda

This pipeline uses Python 2.7, Python ≥3.7, and additional R scripts in a Snakemake pipeline. The provided .yml files will create the appropriate environments, which are completely handled by MPRAsnakeflow. The pipeline is designed to run on a Linux system.

To set up the environment:

Install the general conda environment called snakemake:

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

Activate the snakemake environment:
```
conda activate snakemake
```
To deactivate the environment, use:
```
conda deactivate
```

Quick Test

To verify the installation, run the following command:

conda activate snakemake
snakemake --help