1. Basic Unix Dr Tim Cutts Team Leader Systems Support Group Infrastructure Management Team

2. Why use Unix? Easy to program Easy to automate Lots of software is available for free Flexible Stable Scalable Harder to use than Windows Takes time and effort to learn But your effort will bring rewards!

3. IT at the Sanger Institute Illumina sequencers producing ~200 TB data per week Large Linux clusters to process this data More than 4 petabytes of disk storage More than 100 servers dedicated to providing our websites

4. The UNIX philosophy Portable Multitasking Multiuser Files mostly plain text Lots of small tools which do one job and do it well Command line interpreters which can put these small tools together

5. Unix History 1969 – First version written for a Bell Labs mainframe Unix source code distributed to US government and academic institutions Mid-1970's – First commercial Unix versions 1980's – X11, Unix's graphical interface 1992 – Linux first appears 2000 – Linux starts to gain widespread acceptance in scientific computing

6. Structure of Unix The kernel manages access to all the hardware Command line programs talk to the kernel X11 provides mouse and graphics to programs The shell accepts user commands and starts programs

7. A typical Unix command Unix commands have up to three parts The command name itself: ls Options to modify the command's behaviour: -l The arguments (typically the files you want to work on): *.embl The command is not executed until you press return Wildcards like * are expanded before the program runs: this is different from Windows ls -l *.embl

8. Directories UNIX organises its files very similarly to Windows and Mac OS, in a hierarchy of folders. Each directory [folder] contains two special files:. - represents the current directory.. - represents the directory that contains this one UNIX uses / to separate folder names, in the same way that Windows uses \

9. Filenames in UNIX Filenames in UNIX can contain almost any character But don't do that! All UNIX filenames and commands are case sensitive: ls, Ls and LS are all different Avoid creating files with names containing spaces, or certain punctuation characters Especially anything from: <>$(){}[]#?*:;

10. Handling input and output All UNIX programs always have three files open Standard input – where input comes from (keyboard) Standard output – where output goes to (screen) Standard error – where errors go to (screen) The shell allows you to change these: <Tells the program where to get its input > Tells the program where to put its output | Forms a “pipe” between two programs, so that the output of one forms the input of the next