53  Introduction to the System Shell

This is a very brief introduction to some of the most commonly used shell commands.

A shell is a command line interface allowing access to an operating system’s services. Multiple different shells exist. The most popular is probably bash, which is the default in most Linux installations. In macOS, the default shell switched form bash to zsh in 2019 with the release of Catalina. In Windows, various shells are available through the Windows Subsystem for Linux.

The commands listed here will work similarly in all/most shells.

53.1 Common shell commands

The first thing to look for in a new environment is the help system. In the shell, this is accessed with man:

53.1.1 man: Print the manual pages

For example, the following would return the manual pages for the ls command, explained a little later.

man ls

53.1.2 pwd: Print working directory (the directory you are currently in)

pwd

53.1.3 cd: Set working directory to /path/to/dir 

cd /path/to/dir

53.1.4 ls: List directory contents

ls

adding the -l argument, prints directory contents as a list

ls -l

53.1.5 mv: Move file from /current/dir/ to /new/dir 

mv /current/dir/file /new/dir

53.1.6 mv: Rename file to newfilename 

mv /current/dir/file /current/dir/newfilename

53.1.7 cp: Make a copy of file from currentPath into altPath 

cp /currentPath/file /altPath/file

53.1.8 rm: Remove, i.e. delete, file

rm /path/to/file

53.1.9 mkdir: Create a new directory named ‘newdir’

mkdir /path/to/newdir

53.1.10 rmdir: Remove, i.e. delete, empty directory

rmdir /path/to/somedir

To remove a non-empty directory and all of its contents, you can use rm -rf: -r is recursive; -f is force.

Note: Use with care! it will immediately delete all content in the directory without asking for confirmation

rm -rf /path/to/dir

53.1.11 cat: Print contents of file to the console

cat /path/to/file

53.1.12 uname: Get system information

-a argument for “all”

uname -a

53.1.13 whoami: Print the currently logged in user’s name

whoami

53.1.14 id: Return user identity

The id command returns, among other things, the groups a user belong to. This informs you which directories and files a user can read, write, and execute.

id username

53.2 Running system commands within R

You can execute any system command within R using the system() command:

system("uname -a")

53.3 Useful terminal commands for working with data

If you receive a data file, you may want to get an idea of the contents before reading it into R.

53.3.1 head: Print the first few lines of a file

head iris.csv
Sepal.Length,Sepal.Width,Petal.Length,Petal.Width,Species
5.1,3.5,1.4,0.2,setosa
4.9,3,1.4,0.2,setosa
4.7,3.2,1.3,0.2,setosa
4.6,3.1,1.5,0.2,setosa
5,3.6,1.4,0.2,setosa
5.4,3.9,1.7,0.4,setosa
4.6,3.4,1.4,0.3,setosa
5,3.4,1.5,0.2,setosa
4.4,2.9,1.4,0.2,setosa

You can print the first n lines using the syntax head -n /path/to/file.

For example, you can print just the first line, which would hold the column names in a CSV file:

head -1 iris.csv
Sepal.Length,Sepal.Width,Petal.Length,Petal.Width,Species

53.3.2 tail: Print the last few lines of a file

tail iris.csv
6.7,3.1,5.6,2.4,virginica
6.9,3.1,5.1,2.3,virginica
5.8,2.7,5.1,1.9,virginica
6.8,3.2,5.9,2.3,virginica
6.7,3.3,5.7,2.5,virginica
6.7,3,5.2,2.3,virginica
6.3,2.5,5,1.9,virginica
6.5,3,5.2,2,virginica
6.2,3.4,5.4,2.3,virginica
5.9,3,5.1,1.8,virginica

53.3.3 wc: Word, line, character, and byte count

wc can print the word or line count of a file, among other things. This can be particularly useful when dealing with large files

wc -l iris.csv
     151 iris.csv

The iris dataset consist of 150 cases plus one line with the column names

53.3.4 du: Display disk usage statistics

du can display the size of a file or directory among other things.

This can be very important when trying to determine if the contents of a data file will fit in memory.

Display the size of a file in human-readable format (Kilobytes, Megabytes, Gigabytes, etc)

du -sh iris.csv
4.0K    iris.csv

The same command can be used on an entire current directory:

du -sh .
874M    .

53.4 Further Resources

Bash is the default shell in most Linux distributions.

ZSH replaced Bash as the default shell in macOS with the release of macOS Catalina in 2019 (though Bash currently still comes installed)