Installation

1. Clone the repository:

git clone https://github.com/joncahn/epigeneticbutton.git

to rename it, for example “epicc”:

git clone https://github.com/joncahn/epigeneticbutton.git epicc

2. Move to the directory

cd epigeneticbutton or, if renamed: cd epicc

3. Install snakemake and other required packages from the depency file and activate the environment:

conda create -n smk9 -y --file config/smk9.txt

conda activate smk9

If you don’t have conda yet, follow the directions on the conda website linked here

If you want to run the pipeline on a different platform than locally or slurm, you will need to also install the corresponding snakemake-executor-plugin (executor plugin options here)