Functional Ecological Genomics 2017

Materials for Stephanie Spielman's sessions

Command line Cheatsheet



Directory

  • A folder on your computer which contains files. UNIX filesystems are organized as hierarchical directories.
  • Forward slashes divide levels in the nested hierarchy of directories, e.g. /top_level_directory/second_level_directory
  • The directory at the top of this hierarchy is called the root directory and is denoted simply as /.

Path

  • The address to a directory or file on your computer. There are, generally, two types of paths:
    • Absolute/full path represents the path of a given directory/file beginning at the root directory.
    • Relative path represents the path of a given directory/file relative to the working/current directory.
  • For example, say you have a file “my_favorite_file.txt” located in the directory /Users/myname/Desktop/my_directory.
    • The full path to this file is /Users/myname/Desktop/my_directory/my_favorite_file.txt.
    • The relative path to this file depends on where you are on the computer.
    • If you are calling this file from Desktop, the relative path would be my_directory/my_favorite_file.txt
    • If you are in /Users/myname/, the relative path becomes Desktop/my_directory/my_favorite_file.txt.

Remember - Whenever you call the full path, you can reach the file from anywhere on your computer. Relative paths will change based on your current location.

Basic command line

Command Description
cd Change directory
ls List files and directories in current directory.
pwd Display the path of the current directory (aka print working directory)
rm Remove a file or directory (use rm -r). Warning: This is permanent.
cp Copy a file or directory (original file remains)
mv Move or rename a file or directory (original file is changed)
touch Create an empty file.
mkdir Create a new directory (aka make directory)
echo Print text to STDOUT.
cat Display contents of a file (aka concatenate)
more Display contents of a file, starting at the top and letting the user scroll down.
less Display contents of a file in an even more interactive way, because less is more
head Display the first part of a file.
tail Display the last part of a file.
man Display documentation about a command (aka manual)
clear Clear screen (simply scroll up for past commands). Can also use Ctrl + L

Slightly more advanced command line

Command Description
history View history of recent past commands
sudo Super User do (pronouced “soo-doe”). Explanatory XKCD.
wc Count the number of characters, words, and/or lines in a file (aka word count)
grep global regular
expression parser
sort Sort contents of file
uniq Save only unique lines in file; must be sorted first
cut Select column(s) (i.e. csv or tab-delimited) from a file.
Use argument -f to specify which field(s) to retain and -d to specify the specific delimiter

Shortcuts and symbols

Shortcut/symbol Description
Ctrl + C Kills current process/command
* wildcard character
tab (tab key) autocomplete word
↑ (up arrow) scroll back through previous commands
. Current directory
.. One directory level up
~ Home directory
> Redirect stdout to a file, overwriting file if it already exists
>> Redirect stdout to a file, appending to the end of file if it already exists
| Pipe: redirects stdout to become stdin for next command