Building xaringan slides with Snakemake

TLDR:

1. Install R, Snakemake and xaringan.
2. Navigate to this project's directory and then run: snakemake all --cores 1
   • End result is a html and pdf presentation

Introduction

Repository provides a template to build xaringan presentations to html and pdf using the Snakemake workflow management system. I also manage R's package dependencies with renv.

Motivating Example

I use the Rmarkdown file slides.Rmd which contains the slide template that you would get if you created a new xaringan presentation in RStudio.

Installation Instructions

Follow these Steps to install the necessary software on your system

You need to have the following software and packages installed:

1. Python 3 (Python 3.6 or higher)
2. Snakemake (we'll install it in a couple of lines time!)
3. R (version 4.0.x)

Installing Python

Either:

1. Install Anaconda Python:
   • We provide instructions on how to install anaconda python here
2. Install Python using the deadsnakes ppa (Debian/Ubuntu flavored):
   • Here's how to add the deadsnakes ppa and install Python 3.8

   $ sudo apt-get install software-properties-common
   $ sudo add-apt-repository ppa:deadsnakes/ppa
   $ sudo apt-get update
   $ sudo apt-get install python3.8

Installing Snakemake

I have included a requirements.txt file that we can use to install a specific version of snakemake. This makes sure that my example runs on your machine (or at least won't break because you use a different version of snakemake than I do)

pip3 install -r requirements.txt

you may need to replace pip3 with pip

Installing R

We provide instructions on how to install R here

Installing xaringan

Either:

1. Install it using install.packages('xaringan') in the R console

2. Use our renv workflow:

Open a terminal and navigate to this directory. Then in the terminal enter the following command to install renv:

snakemake --cores 1 renv_install

Then you will need to provide consent for renv to be able to write files to your system:

snakemake --cores 1 renv_consent

Once this is complete you can use renv to create a separate R environment that contains the packages we use in our example by entering the following command into the terminal:

snakemake --cores 1 renv_init

The above command will initialize a separate R environment for this project.

Now we will install the necessary packages (and their precise versions) which are stored in the renv.lock file:

snakemake --cores 1 renv_restore

This will install all the packages we need. It may take a while.

Running the Example:

Navigate to this project's directory, and then run the following command in the terminal:

If you want html and pdf slides:

$ snakemake all --cores 1

If you only want the html presentation:

$ snakemake build_html --cores 1

To get the pdf (you need the html), so use snakemake all --cores 1

Updates to Workflow Example

Major changes are tracked in the NEWS file with brief descriptions of the changes implemented.

Comments / Suggestions / Issues

I'd love to hear your comments, suggestions or installation issues encountered when running the example. Post an issue on Github.

Suggested Citation

Deer, Lachlan. 2021. Building Xaringan Presentations with Snakemake. url = "https://github.com/lachlandeer/xaringan-snakemake"