#acl GoodGroup:admin,read,write,delete,revert CambridgeGroup:read CbuGroup:read

= Your Survival Guide to Unix at the CBSU =

== Commands ==
|| '''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 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'' ||
|| 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. ''grep myfile.txt | ls -l'' ||
|| Changing access permissions || ''chmod'' || e.g. ''chmod 755 <myfile>'' ||
|| Create shortcut for command || ''alias'' || e.g. ''alias cd_batch "cd <mybatchdir>"'' ||
|| Show load of linux boxes  || ''showload'' || ||
|| Change linux box  || ''ssh <machine>'' || e.g. ''ssh l42'' ||
|| Show current processes || ''ps'' || ''ps -ef'' ||
|| Show most CPU-intensive tasks on current processor || ''top'' || ||
|| Checking where an executable file is located || ''which <filename>'' ||  ||
|| Show features of current linux box || ''uname'' || ''uname -a'' ||
|| Check your user name || ''whoami'' || ||
|| Convert text files from DOS to Unix || ''dos2unix <filename>'' || ||
|| Edit files  || ''nedit'', ''emacs'', ''vi'' || ||
|| Help on linux commands || ''man <yourcommand>'' || turn page using space bar, quit typing ''q'' ||

== 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 ||

== 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 [http://imaging.mrc-cbu.cam.ac.uk/meg/Beginners computing-related intros] ||
|| Primer on [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/Primer_ShellScripting shell scripting] ||
|| VNC (http://imaging.mrc-cbu.cam.ac.uk/imaging/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 ||