Software Carpentry: The Unix Shell

• https://swcarpentry.github.io/shell-novice

Time	Activity
8:45	Arrive
9:00	welcome-to-qbb2023
9:30	Summary and Setup
9:45	Introducing the Shell
	Navigating Files and Directories
10:30	Break
10:45	Working With Files and Directories
	Additional Content
12:00	Lunch

Summary and Setup

1. Search for Safari.app using Spotlight
2. Navigate to Software Carpentry’s The Unix Shell lesson
3. Download shell-lesson-data.zip
4. Use Finder.app to move the file to your Desktop
5. Launch Terminal.app

Introducing the Shell

• Summary – Prompt ($), ls, command not found

Navigating Files and Directories

• Summary – pwd, file system, ls -F, <UP><DOWN>, man, cd, hidden files, paths, syntax, <TAB>
• Images
  • 
  • 
  • 
• Exercises
  • Exploring more ls options
  • Listing in reverse chronological order
  • Absolute vs relative paths
  • Relative path resolution
  • ls reading comprehension

Working With Files and Directories

• Summary – mkdir, ls -R, filenames, nano, mv, cp, rm, wildcards
• Exercises
  • Creating files a different way
  • Moving files to a new folder
  • Renaming files
  • Moving and copying
  • Using rm safely
  • Copy with multiple filenames
  • List filenames matching a pattern
  • More on wildcards
  • Organizing directories and files
  • Reproduce a folder structure

Pipes and Filters

• Summary – wc, >, cat, sort, head,

• Images
  • 
• Exercises
  • What does sort -n do?
  • What does » mean?
  • Appending data
  • Piping commands together
  • Pipe reading comprehension
  • Pipe construction
  • Which pipe?
  • Removing unneeded files

Loops

• Summary – for filename in *.dat; do echo $filename; done
• Images
  • for loop pseudocode
  • 
• Exercises
  • Write your own loop
  • Variables in loops
  • Limiting sets of files
  • Saving to a file in a loop - Part one
  • Saving to a file in a loop - Part two
  • Doing a dry run
  • Nested loops

Shell Scripts

• Summary – nano middle.sh, bash middle.sh, $1, #
• Exercises
  • List unique species
  • Why record commands in the history before running them?
  • Variables in shell scripts
  • Find the longest file with a given extension
  • Script reading comprehension
  • Debugging scripts

Finding Things

• Summary – grep, find
• Exercises
  • Using grep
  • Tracking a species
  • Little women
  • Matching and substracting
  • find pipeline reading comprehension