Installation
Installation should take less than 5 minutes
System Requirements
CentOS Linux 7 or above
Required packages
conda (mamba) 4.6 or above
Download here: https://docs.conda.io/en/latest/miniconda.html
snakemake 7.15.1 or above
Download here: https://snakemake.readthedocs.io/
Clone repository
Download here: https://github.com/kircherlab/MPRAsnakeflow.git
Set up conda with snakemake environment
This pipeline uses python2.7 and python3.6 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
mamba 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