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.

You can test if Conda is installed by executing conda --version.

CookieCutter

CookieCutter is a python package that sets up configuration files from project templates. Test if it is installed by executing cookiecutter --version.

If CookieCutter is not installed, execute pip install cookiecutter to install it. It is required later for setting up a snakemake profile

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