Summary and Schedule

This is a new lesson built with The Carpentries Workbench.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Running commands with Snakemake	How do I run a simple command with Snakemake?
Duration: 00h 15m	2. Running Python code with Snakemake	How do I configure an environment to run Python with Snakemake?
Duration: 00h 30m	3. Placeholders and wildcards	How do I make a generic rule? How does Snakemake decide what rule to run?
Duration: 00h 45m	4. Chaining rules	How do I combine rules into a workflow? How can I make a rule with multiple input files? How should I refer to multiple files with similar names?
Duration: 01h 35m	5. Metadata and parameters
Duration: 01h 50m	6. Multiple inputs and outputs
Duration: 02h 05m	7. How Snakemake plans jobs	How do I visualise a Snakemake workflow? How does Snakemake avoid unecessary work? How do I control what steps will be run?
Duration: 02h 20m	8. Optimising workflow performance	What compute resources are available on my system? How do I define jobs with more than one thread? How do I measure the compute resources being used by a workflow? How do I run my workflow steps in parallel?
Duration: 03h 00m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Software installation

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These instructions set out how to obtain and install the software and data on Linux. It is assumed that you have:

• access to the Bash or Zsh shell on a fairly modern Linux or macOS system
• sufficient disk space (~1GB) to store the software and data

You do not need root/administrator access.

Data Sets

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Download the data zip file and unzip it to your Desktop

Software Setup

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Conda

We will use Conda both to install Snakemake itself, and to manage dependencies of our workflows. Miniforge provide a minimal Conda environment, on which we will build.

Details

Download the correct file for your operating system from the Miniforge repository, and execute it at the terminal.

Windows

This lesson has not been tested with Windows. We would recommend using the Windows Subsystem for Linux, and following the instructions for Linux.

macOS, Linux

BASH

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

When prompted, unless you have a reason not to, pick the option for Conda to set up your environment with conda init.

Snakemake

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With Conda available, we can create an environment containing Snakemake and its dependencies. This can be used not just for this lesson, but for your work in Snakemake going forward.

Details

BASH

conda create -n snakemake -c conda-forge -c bioconda snakemake
conda activate snakemake
conda install -c conda-forge 'mamba<2.0.0'

After starting a new terminal, or rebooting your computer, you will need to run

BASH

conda activate snakemake

in order to activate the environment to be able to use Snakemake.