davebiffuk / hpc-intro-sanger

Introduction to HPC for Sanger DTP

Practical introduction to High Performance Computing (HPC)

License

These materials are made available under a Creative Commons Attribution license. This means that you can share and adapt these materials, as long as you give credit to the original materials and authors.

Contributing

The materials are written in markdown. Files are numbered according to their order in the materials sections. Some materials are "extra" and are prefixed with number "99-".

The _site.yml file can be edited to configure the pages that appear on the rendered site. This is necessary if a new file is created and we want to add a new page for it.

The website is built automatically on the gh-pages branch when a new push is sent to the repository. See below for how to build and preview the site locally.

.Rproj and .code-workspace files are provided, if you want to open the folder in RStudio or VS Code, respectively.

Text Boxes

We use some boxes to highlight content, and these can be inserted with the following markdown syntax:

:::note
content here
:::

We have 4 types of boxes available:

• :::note creates an "information" box for side notes, tips and tricks, etc.
• :::highlight creates a box to highlight things like learning objectives or key points
• :::exercise creates a box for exercises
• :::warning creates a box for warnings

Exercises

To create a new exercise, we use the CSS box :::exercise together with an HTML element to hide the answer. Here is an example:

:::exercise

Ask the question here

<details><summary>Answer</summary>

Answer goes here. 

</details>
:::

Build Website Locally

Using RStudio

RStudio already has all the dependencies installed, so you can build the site by setting the working directory to your local copy of the repository and run rmarkdown::render_site() from the console.

From the Terminal

First you need to make sure you have installed:

• R - https://www.r-project.org/
• pandoc - https://pandoc.org/installing.html

Then, install the rmarkdown package:

Rscript -e 'install.packages("rmarkdown")'

Note: On Windows make sure that R is added to Windows PATH.

You can then build the website with:

Rscript -e 'rmarkdown::render_site()'

If there is no error then you will see a _site directory, under which you will find all the html files.