home_precourse.qmd

---
title: "Precourse"
subtitle: "These are steps to be completed before the workshop"
description: ""
date: ""
author: ""
sidebar: false
code-tools: false
number-sections: false
format: html
---

```{r}
#| include: false
library(yaml)
library(here)
upc <- yaml::read_yaml(here("_quarto.yml"))$uppmax_compute
ups <- yaml::read_yaml(here("_quarto.yml"))$uppmax_storage
```

## {{< fa book >}} Coding

We strongly recommend for those not yet familiar with UNIX and/or R/Python to take this opportunity and take these online tutorials, since **those are requirements for the workshop**. This will help you to develop your programming skills and we can always learn a few tricks here and there, even if you are already experienced.

- UNIX: [Part 1](http://swcarpentry.github.io/shell-novice/), [Part 2](https://carpentries-incubator.github.io/shell-extras/)
- R: [Part 1](https://swcarpentry.github.io/r-novice-inflammation/), [Part 2](http://swcarpentry.github.io/r-novice-gapminder/)
- Python: [Part 1](https://swcarpentry.github.io/python-novice-inflammation/), [Part 2](http://swcarpentry.github.io/python-novice-gapminder/)

After taking those courses (or any other equivalent course in programming in bash and R or Python), you should be familiar with

- File structure and manipulation in bash
- Loading, handling and manipulating vectors, matrices, factors and lists
- Creating for-loops
- Using Rmarkdown/Jupyter for reports
- Editing and writing files in the command line
- And much more ...

## {{< fa brands slack >}} Slack

We will use [Slack](https://slack.com/) for communication, troubleshooting and group discussions. Please install [**Slack**](https://slack.com/intl/en-se/downloads). All accepted students will receive an invitation link via email to join the course workspace. Please add this workspace to your Slack application on your desktop rather than using it in the browser.

Once you are in the workspace, please join the following channels:

- `#general` for general questions about the workshop
- `#precourse` for questions related to precourse preparation

::: {.callout-note}
Please post your question in the channel and **NOT** directly to the teacher. Any participant that knows the answer to any problem is encouraged to help too.
:::

## {{< fa server >}} Uppmax

We will use the high performance computing cluster (HPC) UPPMAX for the workshop. You will need to create accounts if you don't already have one. And you will need to join the course projects. See instructions [here](other/uppmax.qmd).

## {{< fa brands docker >}} Docker

If you use Uppmax, you do not need any local installation or setup on your system. If you use Docker, you will need to set up and run Docker yourself. Instructions are [here](other/docker.qmd).

## {{< fa circle-question >}} FAQ

Please refer to the [FAQ](other/faq.html) for troubleshooting common issues.