Download

Overview

This is a relatively short section, as it only covers downloading the required components to run the workflow

The workflow

One the command line, execute git clone https://github.com/JoshLoecker/FastqToGeneCounts.git to download this workflow into the current directory under a FastqToGeneCounts directory

If you would like to download to a specific directory, simply add this name to the end of the command:
git clone https://github.com/JoshLoecker/FastqToGeneCounts a_new_directory

Conda

On almost all high-performance clusters, conda is already installed. If it is not installed on your computer, follow the guide to install it for your system.

CookieCutter

CookieCutter is a python package that sets up configuration files from project templates.

Execute pip install cookiecutter to install it. It is required later for setting up a snakemake profile

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