After cloning this repository, a number of steps (caching the singularity container and data, creating reference files, ...) have to be carried out before starting class. This requires singularity, snakemake and git and has to be executed on a compute node.

On the NIH HPC systems, start an interactive session, load the snakemake and singularity modules, and clone this repository:

user@headnode> sinteractive --cpus-per-task=12 --mem=24g --gres=lscratch:20
...
user@cn1234> ## change to a suitable directory somewhere in /data
user@cn1234> cd /data/$USER
user@cn1234> module load git
user@cn1234> git clone https://github.com/NIH-HPC/snakemake-class.git
user@cn1234> cd snakemake-class

Setup will be different on other systems.

When you are ready run the setup script to fetch data and create all files necessary for the exercies.

user@cn1234> ./setup.sh
...
+------------------------------------------------------------------------------+
|                                                                              |
|                Class materials have been set up successfully                 |
|                                                                              |
+------------------------------------------------------------------------------+

The setup.smk in the root directory of the repo takes care of all the setup required for class. It also serves as another example for a Snakemake workflow.

• Exercise 0 - Singularity refresher
• Exercise 1 - Basic snakemake rules
• Exercise 2 - Parallelizing pipelines
• Exercise 3 - Adding more rules
• Exercise 4 - Running on a HPC cluster
• Exercise 5 - Visualizing workflows