Command Line - Part 1STAT 133

Gaston Sanchez

Department of Statistics, UC–Berkeley

gastonsanchez.com

github.com/gastonstat

Course web: gastonsanchez.com/stat133

GUIs

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Graphical User Interfaces

I Windows and Mac use a Graphical User Interface (GUI) foryou to interact with the OS.

I GUIs are easy to learn

I GUIs rely on visual displays

I GUIs can be extremely useful

I GUIs have improved the friendliness and usability ofcomputers

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GUIs or Command Line?

I However, GUIs come with trade-offs

I They don’t allow you to have more control over what yourcomputer can do

I Some operations are labor intensive and repetitive

I You organize things by clicking and dragging with thecursor (which reduces reproducibility)

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GUI Disadvantages

I Lack of repeatability

I Lack of reproducibility

I Some tasks may be labor intensive using a GUI

I GUIs limit analyses on a cluster of computers

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Command Line

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Command Line

I Instead of using a GUI, we can use a command lineprogram

I The command line program is known as the shell

I By typing commands we perform tasks on the computer(without using a mouse)

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Shell

I You’re working with a program called the shell

I The shell interprets the commands you enter

I It runs the program you’ve asked for

I It coordinates what happens between you and theoperating system

I There are various kinds or flavors of shells: e.g. Bourne(BASH), Korn, C shell

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Command Line

I To interact with the shell we need a terminal emulator

I In Unix-like systems (e.g. Mac) the terminal is usuallyknown as “terminal”

I Windows does not really provide a terminal; instead itprovides the command prompt

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Command Prompt in Windows

Finding MS Windows command promptI Click the Start button

I Click All Programs

I Click Accessories

I Click Command Prompt

Windows command prompt is not a UNIX shell

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Shells for Windows

I Instead of using the command prompt you can use ad-hocshell environments for Windows

I e.g. Git-Bash, PowerShell, Cygwin

I Git for Windows provides a BASH emulation

I PowerShell is part of Windows Management Framework 4.0

I Cygwin is large collection of GNU and Open Source tools

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Mac Terminal

I Go to Applications

I Go to Utilities

I Click Terminal

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Try Some Commands

I date (current time and date)

I cal (calendar of current month)

I df (amount of free space in your disk drives)

I who (logged in users)

I echo ‘Hello’

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Shell

I Shells run in terminal emulators, or terminals

I In Mac OS X, the default reminal program is calledTerminal

I The command line is displayed within the terminal window

I The program behind the terminal is the shell

I There are many different shell programs

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BASH

The most common type of shell is BASH

I BASH: Bourne Again SHell

I BASH is the default shell for Linux

I BASH is usually the default shell on Mac

I type echo $SHELL to see your shell

I type bash to get a bash shell

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BASH

I A shell does much more than simply run commands

I It has wildcards for matching filenames

I It has a command history to recall previous commandsquickly

I It has pipes for making the output of one commandbecome the input of another

I It has variables for storing values for use by the shell

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Command who

I who displays a list of users that are currently logged in

I who am i (whoami) tells you the current user name

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Shell Command Syntax

command -options arg1 arg2

I Blanks and "-" are delimiters

I The number of arguments may vary

I An argument comes at the end of the command line

I It’s usually the name of a file or some text

I Many commands have default arguments

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Date and Calendar

I date

I cal (current calendar year)

I cal july 2015 (July 2015)

I cal jan 2000

I ncal -w july 2015 (week number)

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Options

command -options arg1 arg2

I Options come between the command and the arguments

I They tell the command to do something other than itsdefault

I They are usually prefaced with one or two hyphens

I e.g. ncal -w july 2015

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Some Control Sequences

keys descriptionCtrl + l clear screenCtrl + c stop current commandCtrl + z suspend current commandCtrl + k kill to end of lineCtrl + r search historyCtrl + n next history itemCtrl + p previous history item

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Manual Documentation

I To see the help documentation of a command use manfollowed by the name of the command:

– man cal

– man date

– man who

I q quits manual documentation

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Logging Out

I exit logs you out

I q quits manual documentation

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System Navigation

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Filesystem Reminder

I The nested hierarchy of folders and files on your computeris called the filesystem

I The filesystem follows a tree-like structure

I The root directory is the most includive folder on thesystem

I The root directory serves as the container ofr all other filesand folders

I A Unix-based system (e.g. OS X) has a single rootdirectoyr

I Windows users usually have multiple roots (C:, D:, etc)

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Paths

I Each file and directory has a unique name in the filesystem

I Such unique name is called a path

I A path can be absolute or relative

I An absolute path is a complete and unambiguousdescription of where something is in relation to the root

I A relative describes where a folder or file is in relation toanother folder

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Paths

I There are two special relative paths: . and ..

I The single period . refers to your current directory

I The two periods means your parent directory, one levelabove

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Home Directory

I User’s personal files are found in the /Users directory

I A user directory is the home directory

I cd (with no other arguments) returns you to your homedirectory

I echo $HOME prints your home directory

I cd ∼ takes you to your home directory

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Working Directory

I Another special type of directory is the so-called workingdirectory

I The working directory is the current directory where youperform any task

I pwd prints the working directory

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Changing Directories

I cd

I cd ..

I cd /

I cd ∼I cd ∼/Documents

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Absolute Path Names

/

Ax

B C

D

x

x

directory

file

From the root directory to D:cd /A/B/D

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Relative Path Names

/

Ax

B C

D

x

x

directory

file

Changing directories from D to C

cd ../../C

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Listing Contents in a Directory

I ls

I ls -1 (one entry per line)

I ls -l (list in long format)

I ls -a (show files starting with a dot)

I man ls (manual documentation)

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Listing Contents in a Directory

I ls / (specify root directory)

I ls /usr (specifying a directory)

I ls ∼ (home directory)

I ls -lt (long format, sorted by modification time)

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Listing Contents

/

Ax

B C

D

x

x

directory

file

Show contents in D from Cls ../B/D/

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Inspecting Files

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File Permissions

I run the command: ls -l

I directories may be displayed as: drwxr-xr-x

I files may be displayed as: -rw-r--r--

I file permissions are the 10 most left characters

I r means reads

I w means write

I x means execute

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File Permissions

Read from left to right the permissions mean

position description1 File type. A dash - means a plain file

and d means a directory.There are other less common options.

2-4 Owner permissions: read, write, and executepermissions for the file’s owner.

5-7 Group permissions: read, write, and executepermissions for the file’s group.

8-10 World permissions: read, write, and executepermissions for all other users.

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Type of File

Determine the type of a file:file filename

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Some commands for inspecting text files

I wc filename

I cat filename

I head filename

I tail filename

I more filename

I less filename

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Viewing file contents with less

I There are several commands that display the contents oftext files

I The most commonly used file viewer is less

I less presents the contents of that file on the screen onepage at a time

I There are various keyboard surtcuts to navigate in less

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Viewing file contents with less

key description

Page Up or b scroll back one pagePage Down or scroll forward one pagespaceUp Arrow scroll up one lineDown Arrow scroll down one lineG move to the end of text file1G or g move to the beginning of the text file/hello search forward to next occurrence of hellon search for the next search occurrenceh display help screenq quit less

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Quoting Files

If you want a word to contain whitespace (e.g. a filename witha space in it), surround it with single or double quotes to makethe shell treat it as a unit:ls "My file"

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Exploring a file

I cd into a given directory

I List the directory contents with ls -l

I Determine the contents of a file with file

I If it looks like it might be text, try viewing it with less

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Editing text files at the command line

I Sometimes it is more convenient to create or modify a fileright at the command line

I Although less is a convenient file viewer, it does not allowyou to edit the contents

I Depending on your operating system and shell tool, youmay have one or more command-line text editors:

I e.g. vi, nano, gedit

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Editing text files at the command line

I One common text editor is vi (there’s also vim)

I It should be available in Mac, and also in Git-Bash(Windows)

I Depending on your operating system and shell tool, youmay have one or more command-line text editors:

I Type which vi to fing out if you have it

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Editing text files with vi

I To create and start editing a file simply type vi followed bythe name of the new file:

vi newfile.txt

I Press the I key to start editing content

I When you’re done, press the ESC key

I Then type :wq to save and quit

I You can reopen it again with: vi newfile.txt

Google vi cheat sheet to find more information

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File Management

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Managing Files

Common actions

I creating a directory

I creating a file

I copying a file

I moving a file

I deleting a file

I searching a file

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Managing Files

Common actions

I creating a directory: mkdir

I creating a file: usually through a text editor

I copying a file: cp

I moving a file: mv

I deleting a file: rm

I searching a file: ?

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Creating Directories and Files

Create a directory "summer2015" in my Documents

cd ~/Documents

mkdir summer2015

Create an empty file "README.md" in summer2015

cd summer2015

touch README.md

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Copying Files

I cp is the command to copy files

I cp can be used in two ways:

I cp file1 file2 copies file1 into file2

I cp file1 directory copies file1 into a directory(directory must already exists)

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Copying Files

Copying functions.R from Documents to HW6

cp ~/Documents/functions.R ~/Desktop/HW6/

Copying starwars.csv to current directory

cp ~/Documents/starwars.csv .

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Deleting files

Deleting README.md and starwars2.csv

cd ~/Documents/summer2015

rm README.md

rm starwars2.csv

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Wildcards

I the shell provides special characters to specify filenames

I these special characters are called wildcards

I using wildcards allow you to select filenames based onpatterns of characters

I these wildcards are similar to some regular expressioncharacters

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Wildcards

wildcard description

* matches any characters? matches any single character[characters] matches any character that is

a member of the set characetrs[!characters] matches any character that is not

a member of the set characters[[:class:]] matches any character that is

a member of the specified class

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Example

Create a directory dummy, cd to it, and then create empty files:

$ mkdir dummy

$ cd dummy

$ touch AGing.txt Bing.xt Gagging.text Going.nxt ing.ext

$ ls

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* Wildcard

Use * to refer to multiple files at once; it stands for anything

$ ls

AGing.txt Bing.xt

Gagging.text Going.nxt ing.ext

$ ls G*

Gagging.txt Going.nxt

$ ls *.xt

Bing.xt

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? Wildcard

The question mark ? represents a single character

$ ls

AGing.txt Bing.xt

Gagging.text Going.nxt ing.ext

$ ls ?ing.xt

Bing.xt

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[] Wildcard

Brackets [] can be replaced by whatever characters are withinthose characters:

$ ls

AGing.txt Bing.xt

Gagging.text Going.nxt ing.ext

$ ls [B]ing.*

Bing.xt

$ ls [A-G]ing.*

Bing.xt

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Combining Wildcards

Wildcards can be combined:

$ ls

AGing.txt Bing.xt

Gagging.text Going.nxt ing.ext

$ ls *G*

AGing.txt Gagging.txt Going.nxt

$ ls *i*.*e*

Gagging.text ing.ext

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Test Yourself

AGing.txt Bing.xt

Gagging.text Going.nxt ing.ext

What command produces the output above:

A) ls *ing.*xt

B) ls ?ing.*xt

C) ls ?ing.?xt

D) ls ?ing.xt

E) ls *ing.?xt

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Test Yourself

AGing.txt Going.nxt ing.ext

What command produces the output above:

A) ls *ing.*xt

B) ls ?ing.*xt

C) ls ?ing.?xt

D) ls ?ing.xt

E) ls *ing.?xt

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Wildcard Examples

Pattern Matches

* all filesa* any file beginning with “a”*.txt any file ending with .txt

b*.txt any file beginning with “b” followedby any characters and ending with “.txt”

[gst]* any file beginning with eithera “g”, and “s”, or a “t”

[[:digit:]]* any file beginning with a number[[:upper:]]* any file beginning with an uppercase letter

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