Basic Unix command

Reference - Penn State Roar Useful Unix/Linux Commands

Unix/Linux shells are command line interpreters allowing users to interact with their operating system through utility commands and programs. The Default Unix/Linux shell is BASH (the Bourne-Again SHell) which has extensive online documentation, and common or necessary commands are shown in the table below.

Knowing basic Unix commands should allow you to navigate your Unix or Linux system, confirm the current system status and manage files or directories. It looks very complicated, but once you get familiar with those concepts, it will be beneficial and convenient to operate your analysis in a command-line environment.

Command	Description (For full documentation, use the command 'man command' to bring up the manual or find online documentation)
ls	The 'list' (ls) command is used to display all the files in your current directory. Using the '-a' flag will also show any hidden files (typically files beginning with a '.' like .bashrc)
cd	This is the 'change directory' command. Use this to traverse directories (like 'cd work'). To move back a directory level, use 'cd..'.
mv	The 'move' command takes two arguments, the first being the file to move and the second being the directory said file should be moved to ('mv file.txt /work/newdirectory/'). Note: 'mv' can also be used to rename a file if the second argument is simply a new file name instead of a directory.
mkdir	This command is used to make directories.
rmdir	This command is used to delete directories ('rm -rf directory' would also work).
touch	This command is used to create files in a similar way to mkdir. ('touch test.txt' will create an empty text file named test).
rm	This is the 'remove' command. As mentioned above, it can be used recursively to delete entire directory trees, or it can be used with no flags and a file as the argument to delete a single file.
locate	This command is used to locate files on a system. The flag '-i' will make the query case-insensitive, and asterisks ('*') will indicate wildcard characters.
clear	Clears the terminal of all previous outputs leaving you with a clean prompt.
history	Shows the previous commands entered.
find	Used for finding files, typically with the -name flag and the name of the file.
grep	Used for searching within files.
awk	A programming language typically used for data extraction.
id	Show all of the groups a user is in.
du	Show the disk usage. Typically used with -h (for human readable) and –max-depth=1 to limit to only the directories in that level rather than all files.
env	Print out all of the current environment variables.
less	View a file.
cp	Copy a file. Note the -r (recursive) flag can be used to copy directories.
alias	Create an alias (something short) that is interpreted as something else (a complicated command).
pwd	Print the current working directory.
chmod	Change file permissions.
chgrp	Change group for a file or directory.
ldd	Show the shared libraries required for an executable or library.
top	See the node usage. Often used with command U .
/usr/bin/time	Show time and memory statistics for a command being run. Often used with the -v (verbose) flag.
bg	Continue running a paused task in the background
fg	Bring a background task into the foreground
Ctrl + c	Kill a process.
Ctrl + z	Suspend a process
Ctrl + r	Search through your history for a command that includes the text typed next.

Special Characters

There are some special characters to be aware of that will be helpful.

Character	Description	Example
~	your home directory	cd ~ (change directory to home directory)
.	here	cp ~/data . (copy a file named "data" in your home directory to here (current directory)
..	one directory up	cd .. (go back to one directory up)
*	wildcard	ls *.jpg (list all files in the current directory ending with ".jpg")
|	pipe (send the output to another command)	cat *.txt | grep "Title" (concatenate all txt files in the directory AND find the word "Title"
>	write command output to a file	ls > list (list all files in the correct directory and save that as a file named "list")
man	print manual of the command (you can also try --help)	man ls OR ls --help