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Software Carpentry

Command cheatsheet

Basic commands for Bash (Unix) shell and Git

Bash: navigating the file system

pwd print working directory

ls list directory

  • ls -l: list a lot of file information
  • ls -lh: list a lot of human-readable file information

cd change directory

Bash: interacting with files and directories

mkdir make directory

cat send file or files to output (in most cases, this shows the content of a file without having to open it)

head output first parts of a file or files (default is usually 10 lines)

tail output last parts of a file or files (default is usually 10 lines)

mv rename or move a file or files. Syntax for renaming a file: mv FILENAME NEWFILENAME USE WITH CAUTION!!!

cp copy a file or files. Syntax: cp FILENAME NEWFILENAME

rm remove a file or files. USE WITH CAUTION!!!

Bash: getting information about file contents

wc counts the number of lines, words, and characters in files

  • wc -l: counts only the number of lines
  • wc -w: counts only the number of words
  • wc -c: counts only the number of characters

sort sends an alphabetically sorted list of the contents of a file to output (usually to the screen). Does not change the file itself.

  • sort -n: sorts the output numerically
  • sort -r: reverses the order of the sort, e.g.: Z-A or 10-01

Bash: pipes and filters

* wildcard character that matches 0 or more characters

? wildcard character that matches exactly one character

> redirect output to a new location. Syntax with cat: cat FILENAME1 FILENAME2 > NEWFILENAME USE WITH CAUTION!!!

>> append output to an existing location. Syntax with cat: cat FILENAME1 FILENAME2 >> FILENAME3

| called a pipe. Takes the output of one command and sends it to another command. Syntax with wc, sort, and head: wc -l FILENAMES | sort -n | head -n 1

Bash: syntax of a for loop

for filename in basilisk.dat unicorn.dat
do
head -n 3 $filename
done

Context of this for loop:

  • "filename" is the variable named in the first line and called ("$filename") in the third line of the loop
  • The loop is operating on the two files named in the first line, basilisk.dat and unicorn.dat
  • The third line shows what is being done to the two files; in this case, showing the first three lines of each file.

Basic Git commands

git init: creates a git repository

git status : view the status of your files in the working directory and staging area

git add: tells git to start tracking a file, or a series of files.

git commit: commits (saves) the staged snapshot to the project history.

git log: shows all the commits in the project history

git diff: shows changes made to files

git remote add origin: add a remote repository where changes will be stored, usually for collaboration

git push: sends local changes to a remote repository

git pull: brings changes made in a remote repository to the local repository

Resources

Software Carpentry Bash (Unix) Shell Lesson: http://swcarpentry.github.io/shell-novice/

Software Carpentry Git Lesson: http://swcarpentry.github.io/git-novice/

Source

Author: Jamene Brooks-Kieffer

Affiliation: University of Kansas Libraries

Link: https://github.com/kulibraries/swc-workshop-helps/blob/master/command-handout.md

License: CC-BY https://creativecommons.org/licenses/by/4.0/

Modified from James Baker's original Library Carpentry Git handout: https://github.com/LibraryCarpentry/week-three-library-carpentry-DEPRECATED/blob/master/handout.docx