ctb / hannahs-unix-cafe

Hannah's UNIX Cafe

Hannah's UNIX Cafe

Author: Hannah Houts, @hehouts, UC Davis.

Getting started

Use this to get familiar with the RStudio interface and the unix shell.

Start by opening RStudio.

Log into farm

Use your datalab-XX account to log into farm.

Allocate a compute node

Run:

srun -p high2 --time=3:00:00 --nodes=1 --cpus-per-task 1 --mem 5GB --pty /bin/bash

Install the necessary software

The first time you run this, create a conda environment with the necessary software:

module load mamba

mamba create -y -n cafe r-rmarkdown r-knitr
mamba activate cafe

this will take ~5 minutes.

Every time thereafter, you will need to run the following after srun:

module load mamba
mamba activate cafe

Start up RStudio Server

module load rstudio-server
rstudio-launch 

and follow the process to connect to RStudio Server from your laptop.

R Studio

When you first open RStudio, you'll notice it's divided into several panels, each serving a distinct purpose.

1. Console Panel: This is where R code is executed. You can type commands directly here or run code from a script. It's like a direct line of communication with R.

2. Source Panel: Here, you write and edit files (R scripts, R markdowns, shell scripts). This panel supports features like syntax highlighting and tab-completion to make writing R code easier.

3. Environment/History Panel: The Environment tab displays variables created during your R session, along with their values and types. The History tab keeps a log of all commands you've run, allowing you to revisit and reuse them.

4. Files/Plots/Packages/Help/Viewer Panel: This multifunctional panel has tabs for:

   • Files: Browse, view, and manage files in your working directory.
   • Plots: View graphs and charts you generate with your code.
   • Packages: Install, load, and manage R packages.
   • Help: Access R documentation and help files.
   • Viewer: Display web content or visualizations.

Open the tutorial

Go to the Console panel on the left, and then click on the Terminal. At the terminal prompt, type:

cd ~/
git clone https://github.com/ctb/hannahs-unix-cafe

In the Files panel, you'll see a new folder, hannahs-unix-cafe. Go to that folder and open tutorial.Rmd in RStudio by clicking on it.