Snakemake is a python based workflow management tool. It's very useful when you have a project where you chain a bunch of tools to get a result (e.g. benchmarking your software) and some parts must be distributed in HPC. It also prevents unneccessary re-running.
It would be recommended to use a shared node (16 cores) in Expanse for this tutorial since we will be running stuff.
Requirements: Python and conda
Install mamba to create a conda environment faster.
conda install mamba
Clone this repository and cd to it:
git clone https://github.com/balabanmetin/snakemake-tutorial.git && cd snakemake-tutorial
Then create a conda environment for this tutorial:
mamba create -c conda-forge -c bioconda -n snakeTutorial snakemake-minimal famsa
Activate conda environment
conda activate snakeTutorial
We are ready to go!