= Your Survival Guide to Unix at the CBSU =
What you see below probably seems like a list of arbitrary incantations and may put you off ever going near a unix command line. However, you'll soon find that simple combinations of unix commands (possibly written as a shell script) can do things instantly that would take hours of pointing and clicking on a Mac or PC.

== Commands for Navigation, File Manipulation etc. ==
||'''Function''' ||'''Command''' ||'''Options''' ||
||Show contents of current directory ||''ls'' ||details: ''ls –l'', hidden files: ''ls –a'', output to file: ''ls > file.txt'', wild cards: ''ls *.txt'' ||
||Change directory ||''cd <newdir>'' ||e.g. ''cd /home/myname/mydatadir'', one up: ''cd ..'' (e.g. ''cd ../batchfiles''), to home directory: ''cd ~'' ||
||Make directory ||''mkdir <newdir>'' || ||
||Copy file/directory ||''cp <old> <new>'' ||Copy directories: ''cp -r <old> <new>'' ||
||Move file/directory ||''mv <old> <new>'' || ||
||Delete file/directory ||''rm <filename>'' ||delete directory: ''rm –r <dirname>'', suppress warning prompt: ''rm -f <filename>'' ||
||Create link between a new filename and an existing file ||''ln <filename> <linkname>'' ||symbolic link: ''ln -s <filename> <linkname>'', to see whether a file is "real" or a symbolic link, use ''ls -l'' ||
||Find a file in directory structure ||''find'' ||find ''myfile.txt'' in current directory and below: ''find . -name myfile.txt'', wildcards: ''find . -name \*results\*.txt'' ||
||Find letter string within text ||''grep'' ||''grep error logfile.txt'', ''ps -ef | grep <yourname>'' ||
||See list of previous commands ||''history'' || ||
||Execute command from history list ||''!<x>'', where ''x'' is number in history list ||e.g. ''!112'' to get command 112 from ''history'' list ||
||Send output of a command to text file ||''>'' ||e.g. ''ls -l > listoffiles.txt'', ''>>'' appends instead of overwriting ||
||Send output of a command directly to another command ("pipes") ||''|'' ||e.g. '' ls -l | grep myfile.txt '' ||
||Send output of a command to text file AND standard output (screen) ||''tee'' ||e.g. ''ls -l | tee listoffiles.txt'', ''tee -a'' appends instead of overwriting ||
||Run progress in background (keep command prompt) ||''&'' ||e.g. ''matlab &'', ''runmybatch.sh &'' ||
||Changing access permissions ||''chmod'' ||e.g. ''chmod 755 <myfile>'' or ''chmod go-w <myfile>'' ||
||Changing group of a file ||''chgrp'' ||e.g. ''chgrp imaging <myfile>'' ||
||Create shortcut for command ||''alias'' ||e.g. ''alias cd_batch "cd <mybatchdir>"'', ''alias h history'' ||
||Convert text files from DOS to Unix ||''dos2unix <filename>'' || ||
||Edit files ||''nedit'', ''emacs'', ''vi'' ||e.g. type ''nedit &'' to keep command prompt ||
||Help on linux commands ||''man <yourcommand>'' ||turn page using space bar, quit typing ''q'' ||
||Short description of commands ||''whatis <yourcommand>'' || ||


= System-Related Commands =
||CBU Cluster Utility Functions ||''e.g. login_load, freenodes, showallmatlab'' ||see [[http://intranet.mrc-cbu.cam.ac.uk/computing/cluster-utility/|CBU intranet]]||
||Disk usage information ||''du'' ||''estimate space usage of directories and files, e.g. du –sh /imaging/xy01/experiment1'' ||
||Change linux box ||''ssh <machine>'' ||e.g. ''ssh l42'' ||
||Show your jobs/processes in current session ||jobs || ||
||Show current processes ||''ps'' ||more details: ''ps -ef'' ||
||Kill a process ||''kill'' ||''kill <processID>'', where ''<processID>'' is from ''ps'' output ||
||Show most CPU-intensive tasks on current processor ||''top'' || ||
||Checking where an executable file is located ||''which <filename>'' || ||
||Show name of current linux box ||''hostname'' ||ip address: ''hostname -i'' ||
||Show features of current linux box ||''uname'' ||more details: ''uname -a'' ||
||Check your user name ||''whoami'' || ||
||Get time or date ||''time'', ''date'' || ||


== Useful Tricks ==
||Use cursor keys up/down to get previous commands ||
||Copy/paste: mark text with left mouse button, click to destination, click middle mouse button ||
||Auto-complete commands: start typing, then “Tab” to complete to next unique possibility ||
||Type the beginning of a previously used command, then simultaneously press ''Esc p'' to autocomplete to last used command with same beginning ||
||Move cursor to beginning ''Ctrl+a'' or end ''Ctrl+e'' of command line ||
||Run linux commands from within matlab using ''! <command>'' (e.g. ''! hostname'') or ''[s,r] = unix(<command>)'' (e.g., ''[s,r] = unix('hostname')''), where ''s'' returns the status (0=pass, nonzero=fail) and ''r'' is the result (e.g., 'l41'). ||


== General ==
||Overview of CBU computing: http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners/MatlabIntroCBU?action=AttachFile&do=get&target=RussellComputing.pdf ||
||Computing on Intranet: http://intranet.mrc-cbu.cam.ac.uk/computing/ ||
||Intro to Unix: http://www.ee.surrey.ac.uk/Teaching/Unix/ ||
||More [[CbuMeg:Beginners|computing-related intros]] ||
||Primer on [[CbuMeg:AnalyzingData/Primer_ShellScripting|shell scripting]] ||
||VNC (CbuImaging:UsingVNC): start Putty, ''vncserver –geometry 1280x1024 –name <somename>, for OpenGL graphics: ''vncserver.glx -geometry 1280x1024 -name <somename>'' '' ||
||Access home space: Windows \\home\username; Linux /home/username ||
||Access imaging space: Windows \\samfs-lh\imaging; Linux /imaging/username ||
||32-bit machines:  l21, l24-31, l33-l36, l37-l42;       64-bit machines: l43-l63;     OpenGL machines: l37-l42 ||