Quick Reference

Washington University in St. Louis, School of Medicine

Unix - Quick Reference

Command Syntax	Replace text in italics with your own. Unix is case sensitive. Type return after every command.
command	Plain command with no options or files specified
command -option files	Option modifies behavior of command . See files and directories for format of files.
command -option -option	Multiples options may be used. Consult on-line help.
command file1 -op1 file2 -op2	Options may follow files when different file treatment is possible.

Basic Commands	Commands in parenthesis are aliases that can be used in place of the actual commands.
man topic (or help topic )	Displays information on topic . topic may be a command.
logout (or simply, lo)	Terminates your session on this machine.
passwd	Change password for account. Password is case-sensitive It must be at least 6 alphanumeric characters long it must contain at least 1 number or special character (!, @, #, $, %, ^, &, *, ~, etc.), and at least 2 alphabetical characters.

Files and Directories	Borcim prompt is of the form: {username }borcim: /current_directory {command_number } where current_directory = the directory you are in when you type a command. The command you are about to enter will be denoted by an ascending number, command_number. Full directory paths should be given for files not in the current directory, e.g., /dir1/dir2../file, where /dir1 is the topmost directory (usually the home directory of the user) and /dir2 is a sub-directory under this directory. You may only create directories under your home directory, or in other words, any directory you create must be a sub-directory of your home directory. Note: Home directory is the default directory where you arrive upon login.
~	Abbreviation for the home directory
./	Current directory (where you are)
../	These are system configuration or user defined files that ought not be deleted unless you are sure

Commands	Commands available on Borcim
pwd	Show current directory.
cd	Go to home directory (from anywhere).
cd directory	Changes the current directory to directory . Restriction: directory has to be a sub-directory of the current directory, if not specify path.
cd ../	Change directory to the directory above the current-directory.
cp file new_file	Make a copy of file and call it new_file . You have to specify directory paths to file or new_file if they are in a directory other than the current directory.
cp file ./	Copy file (must specify path) to current directory.
rm file	Delete (remove) file
rm -i file	Delete (remove) file without asking for confirmation.
mkdir dir_name	Make (create) a directory, dir_name (specify path if needed).
rmdir dir_name	Delete (remove) directory, dir_name . Directories cannot be deleted unless they are empty.
ls (or dir)	List all files (and sub-directories) in the current directory.
ls -l	List all files in the current directory with full information, including size, date and permissions.
ls -ld	Show full information on directories. Directory names always have a / at the end.
ls char * (or ls char ??)	List all files in current directory whose name start with char .
cp file new_file	Renames file to new_file . Attach directory paths if needed. mv = cp (copy) + rm (delete).
mv dir1/ dir2/*	Move all files from one directory, dir1 , to another, dir2 . Attach directory paths if needed
apropos keyword	Locate commands by keyword lookup.
set history=n	Remember the last n commands. n =40 is a good number.
history (or simply h)	Display the list of previous commands.
!command_number	Issues a previous command, whose number was command_number
!character	Issue the last command that started with character .

Viewing Files	In the commands below you may substitute type for more and list for cat
more file	Type the contents of file , page (screenful) at a time.
more +line_number file	Start up at line_number of file .
more +/pattern file	Start up file two lines above the first line containing the pattern .
cat file	Type the entire contents of file (and not a page at a time).
grep string file	Search for string in file , where string is word or phrase you want to look for.

Unix Editors	For help on any of the eidtors type help (or man) editor , where editor is one of the editors below.
vi file	Invokes the vi editor and opens up file .
pico file	Invokes the pico editor and opens up file .
emacs file	Invokes the emacs editor and opens up file .

Printing
print file	Print file to MicrobExpress in Room 507. Prints to lw760 for David Schlessinger lab.
lp -dPrinter_name file	To print file to any Unix printer called Printer_name .

Creating Aliases
alias alias *alias-commands*	Create an alias (short cut) , alias, for a command, alias-commands.
alias	List all currently defined aliases. There are some predefined aliases at borcim, like type for more, list for cat, help for man, etc.
unalias alias	Remove alias.

GCG	Commands specific to GCG.
gcg	Command used to initialize the Genetic Computer Groups package. To use GCG specific commands you must initialize the package first.
genhelp	Get a list of all GCG commands. You can then type the name of a given command you want to get help on.
genhelp gcg_command	Get help on a specific gcg_command (that is if you already know its name).
setplot name_of_printer	To redirect the output of plot command (such as plotfold) to a file called PlotPort. If you donÕt issue this command youÕll be able to see the output on a Tek4015 (Versaterm Pro and Telnet 2.6 support this emulation) emulating screen. To go back to viewing the plot on the screen reinitialize GCG by typing gcg. name_of_printer = lw760, for David Schlessinger lab. name_of_printer = MicrobExpress for all other labs.
print PlotPort	This prints the file PlotPort to lw760 for D. Schlessinger lab and to MicrobExpress in Room 507 for all other labs.

Electronic Mail	The mail programs on borcim are available as an alternate to Eudora. Eudora is easier to use, but the Unix mail programs are more secure; no one else can read your mail.
mail	Enter mail program. You can read, reply to, and save mail using this program. Type help for examples on how to use commands.
mail mail_address file	Send mail to mail_address . File is the mail message sent.
pine	Enter pine mailer program. More friendly than mail above.
elm	Enter elm mailer program. As good as pine above.

File protection	Files and directories have independent (r)ead, (w)rite, e(x)execute permissions for owner (u), (g)roup, and world (a). Owner permissions control access for owner (username), group permissions for group access (e.g., labtoxo, huanglab etc.), and world permissions for world (anyone who has an account on borcim) access. You may assign permissions absolutely or symbolically. Type man chmod for help on changing file and directory permissions. Given below are a few examples on how to use chmod to modify permissions symbolically.
chmod u+rwx file	Set read, write and execute permissions for the owner of file.
chmod g-wx dir/*	Take away write and execute (render read-only) group permissions for all files in directory, dir
chmod a+r file	Set read world permissions for file
chmod -R g-rw dir/	Recursively descend through directory, dir , setting the mode for each file as described.
chown owner_name file	Change owner to owner_name of file (file or directory).

Intercommunication	You may not be able to connect to certain hosts depending on the level of security enforced by these hosts.
telnet host_name	Start a session with a TCP/IP host, host_name.
ftp host_name	Start a ftp (file transfer protocol) with a TCP/IP host, host_name.
ping host_name	See if host_name is up or not

Background Jobs	Running a command in the background means that you can type in other commands while itÕs running. To run a command in background, end the command line with an ampersand (&).
command -options file &	Run command in background.
jobs	Lists all jobs running in the background, along with a number for each job and whether its current (running) or stopped.
% job_number	Activates a background job (brings it to foreground), where job_number is the number of the job given by the jobs command.
kill job_number	To abort a background job, where job_number is the number of the job to be aborted.

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Send suggestions and comments to: www@borcim.wustl.edu WWW Department of Molecular Microbiology, Box 8230 Washington University School of Medicine St. Louis, MO 63110-1093 USA		Tel 314-362-7059 FAX 314-362-1232 Last updated February 9, 1996.