Getting Started with Mac OS X/Linux Command Terminal
Ziheng Yang Asif Tamuri
University College London European Bioinformatics Institute
Updated March 2015
What is a Command Terminal?
In the good old days, users interacted with computers
through a command window. This is a text-based
window for typing commands and receiving text-based
output (see screen shot above). Mouse and menu do not
work here but the command line is a powerful interface
and is very convenient for running certain programs.
How do I start a Command Terminal?
On Mac OS X, you can open the Terminal from
Applications>Utilities>Terminal. Alternatively, you can
use the Spotlight search in the top-right corner by
searching for the keyword ‘terminal’.
Commands for manipulating directories (cd,
md)
The OS X or Unix file system consists of a number of directories and sub-directories arranged
hierarchically. The root directory is /. When I start the command terminal, I should be in my home
directory. This may be /Users/ziheng/ or /home/ziheng, etc., depending on the system setup.
The command prompt may show the current (working) directory, as follows: potto:~ ziheng$.
Here I am user ‘ziheng’ on a machine called ‘potto’, and I am in my home directory (which is
indicated by the tilde symbol ~). The dollar symbol $ is the command prompt.
Use cd to change directory. You can use an absolute path containing the entire directory structure.
An absolute path starts with a backslash, which means we begin from the root of the file system.
Without the leading backslash, the directory is relative to your working directory. The tilde
character (~) represents your home directory. Thus no matter where you are,
cd /
will take you to the root directory, and
cd
or
cd ~
will take you to your home directory. Also
cd ~/test
will take you to the test directory inside your home directory.
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cd ..
moves up a level to the parent
directory.
The command pwd prints the current
(working) directory.
To make a new directory called test
in the current directory, type
mkdir test
Getting directory listings (ls)
To list the contents of a directory, type ls
ls -l
The option -l means a long listing. The output may look like the following.
Each line provides the file’s permissions (which we explain later), the owner (ziheng) and group
(staff) of the file, the size of the file in bytes, the date and time the file was last modified and,
finally, the filename.
Wildcards
The special characters * and ? can be used as wildcards when you specify file or directory names.
The asterisk * means any number of any characters while ? means one character of any kind. Thus
ls te*
will list all the files and directories that start with “te”.
ls *.txt
lists all files that end with .txt (the text files).
Copying and deleting files
The commands cp and rm are for copying and removing files.
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cp [Link] [Link]
ls -lF
rm [Link]
ls -lF
Wildcards and relative paths can be used
together. Suppose I have two directories test and test2 in my home directory, and I am
currently in test. Then the first command below will copy all files in the test folder that have
the string fish in their names into the test2 folder, and the second command will delete all files
in test2 that end with .txt.
cp *fish* ../test2/
ls –l ../test2/
rm ../test2/*.txt
ls –l ../test2/
Viewing files on the screen
cat [Link]
less [Link]
less ../test2/[Link]
The command cat shows the content of the file on the screen. This works for plain text files only.
If the file is binary (executables and picture files are for example binary files), rubbish and noise
will pop up. The command less does the same as cat but allows forward and backward
movement within the file using the arrow and page-up/down keys.
Running programs from the command line
Programs are executable files. You run the program by typing the file name at the command line.
The following will run a program called BPP, which is in the bin/ directory under my home
account:
~/bin/bpp
File permissions
drwxr-xr-x 2 ziheng users 4096 Mar 10 14:43 b/
-rw-r--r-- 1 ziheng users 15889 Mar 10 14:43 [Link]
-rw-r--r-- 1 ziheng users 358 Mar 10 14:43 [Link]
The above shows the output from the ls -lF command.
In the first column above, d means a directory while dash (-) means a file. The next 9 fields
specify the file permissions, in which r, w, x, mean readable, writable, and executable while a dash
(-) means no permission. The 9 fields are in three blocks, for user (owner), group and other (world),
respectively. Thus for the file [Link], rw- means the user can read and write but not execute
the file, r-- means the group can read but not write or execute, while r-- means that other
(everyone with an account on the system) can read the file but can’t write or execute it. In other
words, [Link] is readable by everybody (user, group and other), writable by owner only, and
is not executable. Note that you need executable permission to move (cd) into a directory.
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Sometimes the file is an executable program, but you can’t run it if its permission is not set
correctly. This happens often when files are transferred across platforms. In that case you use the
chmod (change mode) command to set the permissions. The following makes program1
executable by user (owner) and group.
chmod ug+x program1
A few tips
Use forward-slash / to specify folders on OS X or UNIX. Use back-slash \ on Windows.
Commands and file and directory names are case-sensitive on OS X or UNIX, while they are
case-insensitive on Windows (MS-DOS).
Given that different fields on the command line are separated by spaces, it is in general a good
practice to avoid using spaces or other strange symbols in file names.
Getting help
Use the command man to view the manual page for any particular command.
man cp
Common useful Windows/Unix commands
Windows UNIX/OSX Function
cd cd Change directory (folder)
md or mkdir md or mkdir make a new directory
dir ls List files and directories
copy file1 file2 cp file1 file2 Make a copy of file1 and name it file2
ren file1 file2 mv file1 file2 Rename file1 as file2
move file1 file2
del rm delete (remove) files
rd rmdir remove an empty directory
time time date and time mean different things in windows
and unix
date date
exit exit exit
help man help or manual
more more show file a screen a time
type cat show file
, , Use the Up & Down arrow keys ( and ) to
, , cycle through past commands. Then use and
or Ctrl- and Ctrl- to move around to
edit.
Tab Tab The Tab key completes file or folder names
> > redirection: screen output will go into file
< < redirection: keyboard input will come from file
| | pipe: output from one program will be input to
the next program
Esc Esc Cancel command
Ctrl-C Ctrl-C terminate job
nice +20 mb run a job at low priority
nice +20 mb & & places the job at the background
Ctrl-Z pause a foreground job
bg place the paused jot at the background