Setup Quarto tutorial#

Setup course material#

Follow this instructions only if you start the course at this stage! Otherwise skip this step!

This tutorial depends on files from the course GitHub repo. Please follow these instructions 
on how to set it up if you haven't done so already.  
Let's create a directory and clone the course GitHub repo.

```bash
mkdir -p  ~/training-reproducible-research-area
cd ~/training-reproducible-research-area
git clone https://github.com/SouthGreenPlatform/training_reproducible_research
```

Setup environment#

First let's create a dedicated folder for this tutorial:

mkdir -p  ~/training-reproducible-research-area/quarto
cd ~/training-reproducible-research-area/quarto
cp -r ~/training-reproducible-research-area/training_reproducible_research/tutorials/quarto/* .

We will use Conda environments for the set up of this tutorial. So, now we will install all the tools via conda:

conda env create -f ~/training-reproducible-research-area/training_reproducible_research/tutorials/quarto/environment.yml -n quarto-env

You can then activate the environment followed by running RStudio in the background from the command lines:

conda activate quarto-env

Rstudio with quarto#

Warning

Quarto is still in its infancy on conda and has some conflicts with certain R packages on conda. What's more, the Rstudio package on conda is not the latest version (does not integrate quarto natively). If you wish to use the graphical interface to generate Quarto files, we recommend the following installations

Docker installation (Reproductible)#

The documentation is available here from the Rocker project.

docker run --rm -ti -p 8787:8787 rocker/rstudio

Classic installation#

Install Rstudio : https://posit.co/download/rstudio-desktop/
Install quarto : https://quarto.org/docs/get-started/

Et voilà !

conda env update -f environment.yml -n quartp-env