= 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'' ||
|| like ''ls'', but can provide lots of SAMFS specific information ||        ''sls'' ||  ''sls –D /imaging/xy01/experiment1/image1.nii'' ||
|| 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'' ||
|| Search for files using specified criteria || ''sfind'' || ''sfind /imaging/xy01/experiment1 –type f –offline –name “*.nii”'' ||
|| 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 =
|| Show load of linux boxes || ''showload'' || ||
|| Disk usage information || ''du'', ''sdu'' || By default, ''du'' will only show online data. ''sdu'' will show on- and off- line data, ''sdu –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 ||
|| Stage offline data back to disk || ''stage'' || ''stage /imaging/xy01/experiment1/image1.nii'' ||
|| 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 [wiki:CbuMeg:Beginners computing-related intros] ||
|| Primer on [wiki:CbuMeg:AnalyzingData/Primer_ShellScripting shell scripting] ||
|| VNC (wiki: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 ||