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Snakemake tutorial

Install miniconda3

If you don't have conda (miniconda, conda or Anaconda) yet, install Miniconda3 MaxOSX 64-bit bash.

bash Miniconda3-latest-MacOSX-x86_64.sh

Follow the prompts on the installer screens and test the installation with:

conda list

and set up your conda channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Download this repo

Then, download this repository to your favourite local computer. If you already have git installed, you can download it with:

git clone https://github.com/crlero/snakemake-tutorial.git
# or
git clone [email protected]:crlero/snakemake-tutorial.git

... otherwise download the ZIP repository from the Code button on the up-right side of this page.

Recreate this tutorial environment

In order to be able to run this workflow example, we must ensure we are running it within a defined environment. To do so, you can either create a new conda environment using the yaml file and download the specific dependencies defined in it or you can activate the environment from the zipped folder that I have placed in the NAS server to speed up the slow stuff :-).

Create conda environment from the .yaml file

cd snakemake-tutorial/handson/
conda env create --name tutorial --file=workflow/environment.yaml
conda activate tutorial

Activate folder with the environment

mkdir environment_tutorial
tar xzvf /Volumes/UserFolders/cristina.leal/snakemake-tutorial/environment_tutorial.tar.gz -C environment_tutorial
source environment_tutorial/bin/activate # activates the environment
source environment_tutorial/bin/deactivate # deactivates the environment

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