Unix Command summary in Unix style

###Unix commands###

# Unix is somewhat abrupt in its phrasing 

files and directories

cp x y 	            # copy file x to y, leaves x
mv x y	            # move file x to y, x is gone!
mkdir x 	    # makes new directory x
rmdir x             # removes a directory
pwd 		    # shows current directory
cd x		    # goes into folder x
rm x 		    # remove file x
ln -s x y	    # makes a soft link between real file x and local pointer y
ls 		    # lists documents in current directory
cat x 	            # list the whole file
more x 	            # types x in chunks, "space" goes to next chunk
less x	            # similar to more
head x 	            # types the first N lines
tail x	            # types the last N lines
find *		    # list all of the files in this directory and below

Process management	

CTL-Z	# pause the current process and return to console
bg 	# allow the process you just paused to run in background
jobs 	# shows what you're running
ps 	# shows processes 

com > file	# output of command com goes to file x
com >& file	# errors from command com goes to file x
com >> file	# appends output of com onto end of x
com >>& file	# appends error of com onto end of x

Help

man com	        # help on command com
com -h	        # sometimes has help this way as well
com --help      # or this

special startup/config files

.login or .profile 	# runs on login
.shrc or .cshrc         # runs when you invoke a script

editing and strings

sed s/a/b/ x > y            # replaces a with b in file x and outputs to y
grep a b	            # print out all lines in  b which contain string a
sort a	                    # sort the file a
diff a b                    # print out the difference between a and b

emacs a	                    # edit the file a

environmentals

environmentals are shortcuts the system will expand for you
very useful if you want to do the same thing with different inputs

In the bash shells  use
export X=y 	        # will make $X refer to y
export PATH=y:${PATH} 	# will append y to $PATH

In the c-shells csh and tcsh
setenv X y      # is the same thing as export X=y
env 		# will list all environmentals you have set
echo $ENV 	# will print the value of $ENV to the terminal

important environmentals are:

$HOST
$USER
$HOME 		        # your home area
$PWD 	             	# the current directory
$PATH 	          	# where unix looks for code to execute
$PYTHONPATH 	        # where unix looks for python modules to import
$LD_LIBRARY_PATH	# where unix looks for shared libraries

you normally want to append to the PATH. Just setting doing export PATH=x
wipes out all the other stuff it was already set to.

export PATH=$FIRST:$SECOND

running scripts

source a      # will just run the commands in file a as if you were typing them
sh  a         # will run the commands but any environment set up within a is gone when it ends

other useful commands - use man or google to see the arguments!!
history       # replays commands you have typed
clear         # clear the screen  

arp, netstat, ifconfing, host, ping, trace route # give you information about your network connections

# alias renames a command to something more convenient

examples from an expert postdoc

alias h="history"
alias hless="history | less"
alias htail="history | tail"
alias ls="ls -Fh"
alias ll="ls -l"
alias llt="ls -lrt"
alias dir="ls -l"
alias la="ls -a"
alias lsa="ls -al"
alias llh="ll -h"
alias cls="clear; ls"
alias rmd="rm *~"  # removes backup files left by some editors