UNIX command line

In this module you will learn:

• What is the computer shell• What is the command line interface• What is the directory tree• Some UNIX commands

The Shell

The shell is a program that provides an interface to the operating system

graphical interface

graphical shell command-line shell

command-line interface

graphical interface

What happens when you double click on the icon of an application?

What happens when you double click on the icon of an application?

command

command-line interfaceprompt

Here you write the command

Open a command-line terminal on your computer

You can type the application name (+ options) in the command-line terminal screen and then type [Return]

command

The directory structure

Root (/)

home bin etc var tmpusr

allegrakristian

courses

applications

data

phospho

tmp

The file-system is arranged in a hierarchical structure, like an inverted tree

The top of the hierarchy is traditionally called root

When you first login, your current working directory is your home directory

• Access you home directory using the command-line interface

• Create a text file “myfile.txt” and save it in your home directory

• Start the gedit text editor

• Go to the command-line interface and type “ls” at the prompt

About UNIX

Everything in Unix is either a file or a process

A process is an executing program identified by a unique PID

(PID = Process IDentifier)

A file is a collection of data

About Unix commands

%rm myfile.txt [Return]

• The shell searches the file containing the program rm• executes the program rm on myfile.txt • After the process rm myfile.txt has finished running, the shell returns the prompt % to you, indicating that it is waiting for further commands.

Commands are themselves programs

Here you can type a new command

General remarks

• If you've made a typo: CTRL-u to cancel the whole line

• Unix is case-sensitive

• There are commands that can take options

• The options change the behaviour of the command

• UNIX uses command-line completion

• %command_name -options <file> [Return]

• %man <command name> [Enter]

• %whatis <command name> [Enter]

General remarks

• CTRL-A sets the cursor at the beginning of the line

• CTRL-E sets the cursor at the end of the line

• You can use a text editor to write stuff

• You can use up and down arrows to recall commands

• The command whereis tells you where is a given program

General remarks

Listing files and directories

The directories ‘.’, ‘..’, and ‘~’

% ls -a [Enter]

% cd . [Enter]

% cd .. [Enter]

% ls ~/oeiras

Handling files and directories

clearlessmore

Redirection

File system security (access rights)

-rwxr-xr-- 1 gould admin 2541 2009-08-19 16:57 new_scop.txt

Each file (and directory) has associated access rights, which may be found by typing ls -l

permissions

number of links

owner

group owner

size in bytes

date and time of the last modification

file's name

r allows users to list files in the directoryw allows users to delete files from the directory or move files into itx allow users to access files in the directory

Access rights on directories

d

Changing access rights: chmod

%chmod go-rwx myfile.txt%chmod a+rw biglist

Running your program from the command line

%python test.py

%pymol

%chmod a+x test.py%test.py BUT: #!/usr/bin/python

Processes and Jobs

Backgrounding a current foreground process

Listing processes

A process may be in the foreground, in the background, or be suspended

Backgrounding a long process has the effect that the Unix prompt is returned immediately, and other tasks can be carried out while the original process

continues executing

% sleep 10 & [Enter]

% sleep 100[Ctrl Z] (^Z shortcut)% bg

Running background processes

% ps #list of processes with their associated PID and status % jobs #list of running processes% fg %jobnumber #restart (foreground) suspended process% fg #restart(foreground) the last suspended process

UNIX Variables

% echo $OSTYPE

shell variables apply only to the current instance of the shell and are used to set short-term working conditions

environment variables have a farther reaching significance, and those set at login are valid for the duration of the session.

Variables are a way of passing information from the shell to programs when you run them

Some are set by the system, others by you, yet others by the shell, or any program that loads another program

When you type a command, your path (or PATH) variable defines in which directories the shell will look to find the command you typed.

If the system returns a message saying "command: Command not found", this indicates that either the command doesn't exist at all on

the system or it is simply not in your path.

Setting the path

set path = ($path /Applications/blast/)

To add this path PERMANENTLY, add the line to your .cshrc AFTER the list of other commands

setenv PATH ${PATH}:/Applications/Blast

Transferring files between and connecting to remote hosts

% scp <SourceFile> <user@host:directory/TargetFile>

% scp <user@host:/directory/SourceFile> <TargetFile>

% sftp <user@host>password:$ cd <directory>$ get TargetFile$ put SourceFile

wget [option]... [URL]...

[URL]: http://host[:port]/directory/fileftp://host[:port]/directory/file

% ssh user@hostPassword: