Info

This page will serve as a collected reference of the commands introduced in the lecture videos and slides. It is not intended to replace the man pages or watching lectures or reading over the slides, but will hopefully help you navigate the commands we have shared.

Info

Some commands have a “relevant flags” section with flags used in lecture/homeworks prior to the current homework. They serve as a place to start looking - but you should still read the man page to see what these flags do. Importantly, this does not include flags we expect you to discover in the “self-discovery” portion of a homework!

Linux Commands

Basic Shell Commands

Command Lecture Description
ssh 01 Log in to a remote Linux server (e.g., attu)
pwd 01 Print current working directory
cd 01 Change working directory
ls 01 List files in working directory
(relevant flags: -a -l -r)
man 01 Bring up manual for a command
exit 01 Log out of shell
xargs 03 Converts standard input to command line arguments
(relevant flags: -d)
tee 03 Allows for the output of a command to be redirected to both a file and stdout

System Commands

Command Lecture Description
clear 01 Clears all output from console
date 01 Output the system date
cal 01 Output a text calendar
uname 01 Print information about the current system

Directory Commands

Command Lecture Description
ls 01 List files in working directory
pwd 01 Print current working directory
cd 01 Change working directory
mkdir 01 Make a new directory
rmdir 01 Remove the given directory (must be empty)

File Commands

Command Lecture Description
cp 01 Copy a file
(relevant flags: -i)
mv 01 Move a file (also used to rename files)
(relevant flags: -i)
rm 01 Remove the given file
(relevant flags: -f -r)
touch 01 Create empty file, or change time-modified
chmod who(+-)what filename 08 Change permissions for filename (e.g., give owners/group read/write, others).
Example: chmod ug+rw,o-rwx file.sh
chmod NNN filename 08 Change permissions for filename using octal codes. Digits correspond to owner(u), group(g), others(o) respectively (+4 for read, +2 for write, +1 for execute).
Example: chmod 660 file.txt
umask [options] [mask] 08 Sets the default permissions of files, calling umask similarly to chmod with octal will remove those permissions for newly created files (start with a leading 0 to indicate base 8 e.g. umask 0022)

File Examination Commands

Command Lecture Description
cat 02 Print contents of a file
less 02 Output file contents, one page
more 02 Output file contents, one page
head 02 Output number of lines of start of file
(relevant flags: -n)
tail 02 Output number of lines of end of file
(relevant flags: -n)
wc 02 Count words, characters, lines in a file
(relevant flags: -l -w)

Searching and Sorting Commands

Command Lecture Description
grep 02 Search given file for pattern
(relevant flags: -E -i -o -v)
sort 02 Sort input or file, line based
(relevant flags: -f -r)
uniq 02 Strip duplicate adjacent lines
find 02 Search filesystem
(relevant flags: -type)
cut 02 Remove section from each line of file
sed -r 's/REGEX/TEXT/' 07 This will replace all matches of REGEX in the given file with TEXT and output it to the console.
(relevant flags: -i)

Users

Command Lecture Description
whoami 08 Print your username
id 08 Print user ID and group membership
users 08 List logged-in users (short)
who 08 List logged-in users (long)
pinky 08 Print information about users

Groups

Command Lecture Description
groups 08 Print group membership
groupadd 08 Create a group
groupdel 08 Delete a group
groupmod 08 Modify a group
chgrp 08 Assign to group
chgrp -R . 08 Changes all files recursively starting in the current directory to be owned by

Processes

Command Lecture Description
ps 08 List processes being run
(relevant flags: -u)
top 08 Show process statistics
kill 08 Terminate process by PID
killall 08 Terminate process by name

Java Commands

Command Lecture Description
javac ClassName.java 02 Compile ClassName
java ClassName 02 Run ClassName

Unix File System

Relative Directories

Command Lecture Description
. 01 References the working directory
.. 01 References the parent of working directory
~username 01 username's home directory
~/Desktop 01 Your desktop

Unix File System

Command Lecture Description
/ 01 Root directory that contains all directories
/bin 01 Applications/programs (i.e. binaries)
/dev 01 Hardware devices
/etc 01 Configuration files
/home 01 Contains user's home directories
/proc 01 Running programs (processes)
/tmp, /var 01 Temporary files
/usr 01 Universal system resources
Directory permissions 08 Directories have the same permissions as files but read determines viewing privileges, write determines add/delete file privileges, and execute determines whether a user can enter the directory.

Text Editors

Command Lecture Description
nano 01 Very simple editor
vim 01 More advanced text-editor
emacs 01 More advanced text-editor

Vim Basics

Command Lecture Description
:w 01 Write (save) the current file
:wq 01 Write (save) the current file and exit
:q! 01 Quit, ignoring all changes
i 01 Go into insert mode
Esc 01 Go back to normal mode
hjkl 01 Move cursor left, down, up, right
u 01 Undo last change
x 01 Delete character

Emacs Basics

C = control key, M = alt/meta key

Command Lecture Description
C-x C-f 01 Read a file into emacs
C-x C-s 01 Save a file to disk
C-x C-c 01 Exit emacs
C-s 01 Search forward
C-r 01 Search backwards
C-v 01 Scroll to next screen
M-v 01 Scroll to previous screen
C-x u 01 Undo

Bash Scripting

Running a shell script

Command Lecture Description
#!/bin/bash 09 At top of file, tells the command line how to interpret your file
chmod +x script.sh 09 Gives script.sh execute permissions so it can be run with ./script.sh

Variables

Command Lecture Description
CLASS="391" 09 Creates a variable (no spaces on either side of = sign) (variable names are case sensitive)
echo "I am taking $CLASS" 09 Variables are referenced using the $ operator (output: I am taking 391)
echo 'I am taking $CLASS' 09 Single quotes will not expand variables (output: I am taking $CLASS)
contents=$(ls) 09 The output of running a command can be saved to a variable and referenced later

Command Line Arguments

Command Lecture Description
$0 09 Name of the script
$1, $2, $3... etc. 09 First, second, third arguments
$# 09 Number of arguments
$@ 09 List of all arguments

Arithmetic

Command Lecture Description
let SUM="$a + $b" 09 Use let expression to do arithmetic (bash supports multiplication, division, addition, and subtraction)
PRODUCT=$(( $a * $b )) 09 Other way to do arithmetic, must have spaces in between operations!

For Loops

Command Lecture Description
for i in $(seq 1 4); do; echo $i; done 09 For loop syntax, begins with do and ends with done. Semicolon is the same thing as a new line.
for file in $(ls); do; echo $file; done 09 Iterates over all of the files in the current directory by iterating over output of ls

If Statements

Command Lecture Description
if [ $a -lt $b ]; then
  echo "a is < b"
else
  echo "a is not less than b"
fi		 09 If statement basic syntax. Boolean expression must be surrounded by [ ] with spaces on either side.
-gt, -lt, -ge, -le, -eq, -ne 09 greater than, less than, greater than or equal to, less than or equal to, equals, not equals
-a 09 And operator. Can also be written (if [ expr1 ] && [ expr2 ]; then)
-o 09 Or operator. Can also be written (if [ expr1 ] || [ expr2 ]; then)
if [ ! expr1 ]; then 09 Negates expr1
=, != 09 Test if string is equal (=) or not equal (!=)
-z, -n 09 Test if a string is empty (-z) or nonempty (-n)
-f, -d 09 Test if a file (-f) or directory (-d) exists
-r, -w, -x 09 Test if a file exists and is readable (-r), writeable (-w) or executable (-x)

Exit Codes

Command Lecture Description
$? 09 Variable containing exit status of previously run program. It will be 0 if the program executed correctly, or not 0 if it failed.

Input/Output Redirection and Command Substitution

Command Lecture Description
command < filename 02 stdin redirection: execute command and read its standard input from the contents of filename instead of from the console.
command > filename 02 stdout redirection: execute command and redirect its standard output to the given filename
command 2> filename 02 stderr redirection: execute command and redirect its standard error to the given filename
command 2>&1 02 stderr redirection: execute command and redirect its standard error to standard output
command 2>&1 > filename 02 stdout and stderr redirection: execute command, redirect standard error to standard output, and redirect standard output to filename
command1 | command2 02 Pipes: execute command1 and send its standard output as standard input to command2.
command1 ; command2 03 "THEN": Execute command1, then execute command2
command1 && command2 03 "AND": Execute command1, and if it succeeds, then execute command2
command1 || command2 03 "OR": Execute command1, and if it fails, then execute command2
$(command) 03 Command substitution: execute command, then place the output string literally into the given context e.g. `javac $(find -name "*.java")`
alias = 08 Creates alias for (do NOT put spaces surrounding the equals)
.bash_profile 08 Everytime you log in to a shell (i.e. by ssh-ing into attu or logging into your computer), the commands in ~/.bash_profile are run
.bashrc 08 Everytime you launch a non-login shell (i.e. by launching a new terminal) the commands in ~/.bashrc are run.
$PATH 08 Stores the path to all directories which the system will look for programs to run. If a path is in $PATH and contains a file named , will be run when you type
export PATH=/your/new/directory:$PATH 08 Prepend a directory to your $PATH (directory will be looked through first for a filename matching when )
export PATH=$PATH:/your/new/directory 08 Append a directory to your $PATH (directory will be looked through last for a filename matching when )

Git Commands

Command Lecture Description
git clone url [dir] 04 Copy a git repository
git add file1 file2... 04 Adds file contents to staging area
git stage file1 file2... 04 Same as git add
git commit 04 Takes a snapshot of staging area and creates a commit
git status 04 View status of files in working directory and staging area
git diff 04 Show difference between staging area and working directory
git log 04 Show commit history
git pull 04 Fetch from remote repository and try to merge
git push 04 Push local repository to remote repository
git branch <branch> 04 Create a new branch with given name
git checkout <branch> 04 Switch to the given branch
git switch <branch> 04 Switch to the given branch
git merge feature 04 Merges the feature branch into the current branch checked out
git log --graph --oneline 04 View the commit history, and where HEAD and master are located. Flags unnecessary

Regex Syntax

Command Lecture Description
. 06 Matches any character
^ 06 Matches start of line
$ 06 Matches end of line
\< 06 Matches start of word
\> 06 Matches end of word
\ 06 Escape the following character
| 06 Logical or operator (match this character set or that character set)
* 06 Matches zero or more of the preceding character set
+ 06 Matches one or more of the preceding character set
? 06 Matches zero or one of the preceding character set
() 06 Group characters together
[] 06 Character set
[^] 06 Negate character set
[a-z] 06 Matches all lowercase letters
[A-Z] 06 Matches all uppercase letters
[0-9] 06 Matches all digits
\1 06 Back references the same characters captured in an earlier grouping (specified by the number), up to \9
{} 06 Specify how many occurrences of a match we want. Can be an exact number (i.e. {N}) or an inclusive range of numbers (i.e. {MIN,MAX}).