Introduction to Bio-Linux

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home/user1 The name of the base file folder, the one within which everything else is, is “/”, usually referred to as the “root directory”. /home /home/user home is a file folder located within the root directory user is a file folder within the directory home which is within the root directory All the directory names are separated with a forward slash – so the directory user1 is located within the directory home, which is within /. The real power on Linux/Unix systems is the command line. You usually access the command line from within terminals. You can open a terminal by: • clicking on the icon on the top tool bar • right-clicking on the desktop and choosing the menu option “New terminal” • or by going to the Utilities option under the Programs drop down menu, and choosing Terminal You can also start new terminals by typing their name on the command line. There are in fact a number of different types of terminals – each type has its own idiosyncrasies. The terminals brought up by clicking on the terminal icon are called “gnome-terminals”. You can start one from the command line by typing: gnome-terminal & The & allows you to keep working in the original window by starting up the process, (in this case, a gnometerminal), and putting that process in the “background”. If you want to know more about this, please ask a demonstrator. Listing files in a directory Use the ls command to list files in a directory By default, the command will list the filenames of the files in your current working directory. At the moment, this is your home directory. If you add a –l after the ls command, it alters the behaviour of the command – it will now list the files in your current directory, but with details about them including who owns them, what the size is, what kind of file it is, etc. There are many options that modify what information is returned by ls. To find out about them, you can refer to the manual pages for this command by typing: man ls By giving the name (or full path) of a directory you wish to list the contents of, you can find out what is in directories other than the one you are running your command from. ls /usr/local/bin ls –lR /usr/software 2
You can also use regular expressions to limit the files you wish to list. * means any character ? means a single character [ ] can be used to designate a group of characters Exercise List the files in your current directory. Compare this to what you see in the file manager. List the files in your current directory with full details. List all the files in the directory intro_pract. Click on the icon for the intro_pract directory in the file manager and compare the output of the ls command to what you see. List all the files in the directory intro_pract. that start with the letters tes ls intro_pract/tes* List all the files in your directory that start with tes, and end in 1.embl, 2.embl or 3.embl ls intro_pract/tes*[1-3].embl Changing the look of the terminal If you don’t like the colour scheme of the terminal you are working in, you can change it using the Preferences option under the Settings menu on the terminal. Exercise Go to the Preferences option under the Settings menu on the terminal. Choose the panel Colours, and then choose the colour scheme you want. Please note that the option “black on white” actually produces black on grey. To get black print on a white background, choose Custom Colours and choose the colours you want. After this, any new terminal you open will inherit your new colour scheme. Pressing the right hand mouse button can bring up menus of options for the terminal you are working in. You can close terminals by typing exit on the command line or choosing Exit under the File menu. There is also a menu under the tiny icon to the left of the word Terminal at the top of your terminal window. Try out some of the options. Try choosing the option Sticky under Toggle. This makes that terminal appear in every virtual desktop, instead of just one desktop. Note: please use the exit options mentioned above to close your terminal, rather than the Close option in this menu. 3
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Introduction to Bio-Linux

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