1. Getting Started

Prepare the environment¶

Connect to Biowulf and load an interactive session

# login
ssh -Y $USER@biowulf.nih.gov

# load interactive session
srun -N 1 -n 1 --time=12:00:00 -p interactive --mem=8gb  --cpus-per-task=4 --pty bash

Clone the Repo¶

Clone the github repo

cd /path/to/working/dir

git clone https://github.com/slsevilla/snakemake_tutorial.git

cd snakemake_tutorial

Completing the Activty¶

Two diretories were created within the repo. The pipeline_todo directory should be used to complete the tutorial, editing all files as needed. The pipeline_example directory has the activity completed and should be used a reference for completing each of the tasks.

NOTE: There are multiple ways to complete each rule, so review the expected outputs within the pipeline_example/output directory if your code varies.