Using the Shell

Objectives

Understand the what and why of the shell
Use the shell to navigate your computer’s file system
Use RStudio projects to simplify file system navigation
Know your options for finding help

Lesson outline

Review of last week
- What happened as you were trying to re-organize projects or R code? Victories? Stumbling blocks?
Slides: Intro to the shell
- What is the shell?
- What does the shell let us do?
- Why would we want to learn how to use the shell?
Breakout rooms: Shell installation
- Instructor notes include links to git installation for both Mac and Windows.
- Split into 2 breakout rooms to install on different OS’s.
Break to all download shell-lesson-data
- Link
- Put it on your Desktop
- Unzip using point-and-click
Live coding: Setup RStudio
- Open RStudio
- Tour panes: files and terminal
- Set up terminal pane to use bash
Live coding: Navigating filesystems in files pane
- Use file pane to navigate to shell-lesson-data
Live coding: Navigate to shell-lesson-data in Terminal
- Identify the prompt and note that it is different in zsh (%)
- pwd
- cd
- ls
  - Use ls flags to explain anatomy of a shell command
  - Show man ls to show flag options for the ls command
Live coding: Synchronizing file panes
- Show “Go to current directory” to bring Terminal to files pane
- Show “New terminal here” to create a terminal in files pane
- Show that Rstudio’s working directory is not automatically wherever either Terminal or the file pane is
Live coding: using Rprojects to simplify filesystems
- Create an R project
- Show that, upon opening, Terminal, getwd(), and file pane are all on the same page
Live coding: cp and move
- Copy shell_lesson_data to the Rproject.
- Tell them we need cp, then use cp --help to get the options
- Repeat using ls to explore contents of shell_lesson_data and mirror files pane
Live coding/discussion: options for finding help
- --help flag
- man pages
- Manual pages: ? in R, package websites
- StackOverflow
- ChatGPT
Homework for next session
- Read https://peerj.com/preprints/3159/ git (Version control prep)
- Create a diagram of your file system and note your most frequently used directories

Installation & materials

Slides
macOS git installation
Windows git installation (detailed step-by-step here)
Software Carpentry Unix Shell episode #1
Software Carpentry Unix Shell episode #2
Software Carpentry Unix Shell episode #3 (time permitting)

Citation

BibTeX citation:

@online{scott2024,
  author = {Scott, Eric and Diaz, Renata and Guo, Jessica and Riemer,
    Kristina},
  title = {Using the {Shell}},
  date = {2024},
  url = {https://cct-datascience.github.io/repro-data-sci/lessons/3-shell/notes.html},
  doi = {10.5281/zenodo.8411612},
  langid = {en}
}

For attribution, please cite this work as:

Scott, Eric, Renata Diaz, Jessica Guo, and Kristina Riemer. 2024. “Using the Shell.” Reproducibility & Data Science in R. 2024. https://doi.org/10.5281/zenodo.8411612.