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Notes on Linux operating system
Written by Jan Mrázek for the MIBO(BCMB)8270L course
last updated: Jan 9, 2007

UNIX: operating system
Linux: free version of UNIX
Basic communication with a Linux computer is through a command line terminal (no graphics) or
“shell”
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Most modern UNIX/Linux platforms offer a graphical user interface similar to Windows but its use
over the network can be problematic
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One of the advantages of using Linux and Linux shell is that you can access the computer from
anywhere through the Internet
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If you want to use your home computer for
access to our server download and install SSH 3
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9 at http://www
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uga
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2
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For the purpose of this course you have
been provided with accounts on our lab server willow
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uga
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ssh allows you to open a Linux shell window on your desktop
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ssh itself does not allow
you to move files between your computer and the remote Linux computer
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Linux file system
Files in Linux are organized in directories (analogous to folders in Windows)
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Users have their files in their home directories in “/home/”
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Special directory names: “
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/” refers to the directory one level
above the current directory; “~/” refers to your home directory
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That is, the file names “MyFile”, “Myfile”, “myfile”, and “MYFILE” relate to four different files
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” (period) are hidden files
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Under normal situations you don’t have to
worry about the hidden files
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” at the start of a file name
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Basic types of access are read, write and execute
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g
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Write access allows you to delete, modify or overwrite files
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You have write access only to your home directory, that is, unless specifically given access you
will not be able to store files elsewhere on the file system
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File permissions
can be changed with the “chmod” command but it is unlikely that you will need it in this course
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” in file names
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txt,
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bat, etc
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I recommend that you use directories to keep your files organized
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Most useful are “*” (matches
any text) and “?” (matches any single character)
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z” but not “a2
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You can use it with directories, too, e
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, the command “ls
~/*/*
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txt” in directories one
level inside your home directory
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For example, “ls /home/jan” will list the
content of my home directory (“/home/jan” is a parameter)
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“cp file1 file2” will read “file1” and make a copy named “file2”
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In addition to parameters, most Linux commands have options
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For example,
“ls -l /home/jan” will list additional information about each file (without the -l it will only list the
file names)
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There are several types of shells that have some minor differences
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List of Basic UNIX/Linux shell commands
Following is just the very basic list of some useful commands
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g
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Check http://linux
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mt/article/terminal for a
beginner’s tutorial including some more advanced tricks
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E
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, “ls >
List” will list all files in the directory but store it in a file named “List” instead of displaying it on
the screen
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Files and directories
• pwd: shows current directory
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cd with no parameters
switches to your home directory
• ls directoryname: lists contents of directories
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You can limit the list with wildcards (e
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, “ls /home/mydirectory/*
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• cp source destination: makes a copy of a file named “source” to “destination”
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• rm filenamelist: removes/deletes file(s)
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• rm –r directory: removes directory (-ies) including its content
Viewing files
• cat file: prints the whole file on the screen
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g
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You can also use wildcards, e
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, “cat *
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• more file: shows a file page by page
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These
are just few things you can do with more
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Scroll up
and down as in more
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• Many commands will show basic description when run with -h or --help option
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This allows you to set access to your files
for other users or turn a text file into an executable
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• cc program
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~/bin/ is a standard place for storing executable
(binary) files
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–O option will
optimize the program (make it run faster)
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However,
they take a while to get used to and unless you already know them you may be better off using sftp
to open the file in Notepad on your (Windows) computer
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Running programs
Once created, executable programs can be run as any regular command just by typing the program
name and any parameters and/or options
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Executable program files can be created in different ways (included for your reference):
• When written in a language like C, C++, or Fortran, the “source code” (human-readable text
file prepared by a programmer in an appropriate syntax) can be converted into an
“executable” (machine-readable binary file) by a special program called compiler (see cc
command above)
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Program packages are increasingly often distributed as rpm files where the
installation is completely automatic making it very easy for the user (generally only the
system administrator can install such packages)
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That will effectively turn them into executable programs
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This
makes such programs slower to run but eliminates need for compilation
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