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Setup Snakemake tutorial#

Setup course material#

Follow this instructions only if you start the course at this stage! Otherwise skip this step! 
This tutorial depends on files from the course GitHub repo. Please follow these instructions 
on how to set it up if you haven't done so already.  
Let's create a directory and clone the course GitHub repo.

```bash
mkdir -p  ~/training-reproducible-research-area
cd ~/training-reproducible-research-area
git clone https://github.com/SouthGreenPlatform/training_reproducible_research
```

Setup environment#

First let's create a dedicated folder for this tutorial:

mkdir -p  ~/training-reproducible-research-area/snakemake
cd ~/training-reproducible-research-area/snakemake
cp -r ~/training-reproducible-research-area/training_reproducible_research/tutorials/snakemake/* .

We will use Conda environments for the set up of this tutorial. So, now we will install all the tools via conda:

conda env create -f environment.yml -n snakemake-env
conda activate snakemake-env