02 - Setup
Table of contents
Install Miniconda
For this workshop, will analyse our data using various software. However, the only software we will need to manually install is Miniconda.
Check your OS
If you already use Linux or MacOS X, great! Ignore this paragraph!. If you use Windows, setup a Linux virtual machine (VM) with Vagrant (see instructions on how to do this here).
Installing miniconda
Information on how to install Miniconda can be found on their website. Snakemake also provides information on installing Miniconda in their documentation
Once miniconda is installed, set up your channels (channels are locations where packages/software are can be installed from)
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Create a conda environment
With Miniconda, we can create a conda environment which acts as a space contained from the rest of the machine in which our workflow will automatically install all the necessary software it uses, supporting the portability and reproducibility of your workflow.
Create a conda environment (called demo_workflow_env) that has python and Snakemake installed (and all it’s dependant software)
conda create -n demo_workflow_env python=3.7.6 snakemake=5.28.0
Respond yes to the following prompt to install the necessary software in the new conda environment:
Proceed ([y]/n)?
Activate the conda environment we just created
conda activate demo_workflow_env
Now we can see which conda environment we are in on the command line
(demo_workflow_env) lkemp@Wintermute:~$
Snakemake has been installed within your demo_workflow_env environment, so you won’t be able to see or use your Snakemake install unless you are within this environment
Clone this repo
To clone this repo (and use the example data I have provided), you will require you have git installed. See this guide for help with an installation of git.
Once git is installed, clone this repo with the following:
git clone https://github.com/leahkemp/RezBaz2020_snakemake_workshop.git
cd RezBaz2020_snakemake_workshop
See the Git Guides for information on cloning a repo