To the beginner

ls: lists all visible files in the current directory.

Try: ls -ltrh

to view files with long printing (l), last modified sorting (t), in reverse (r), and human readable (h) file sizes.

Try: ls .*

to view all hidden files that start with ‘.’ such as .bashrc.

Try: ls /

to view all files in first layer of subdirectories, etc.

Try: ls */ -d

to view all files that match a wildcard with a directory.

cd: change directory.

Try: cd ~/

to change directory to home

Try: cd -

to change directory to the previous one.

Try: cd ../

to move up one directory

mkdir: make a directory.

Try: mkdir -p path/to/directory

to simulatenously make new directory path, with a subdirectory inside to, with sub-subdirectory inside called ‘directory’

pwd: gets the current working directory.

clear: clear the terminal screen

man: Help manual

Try: man rm

touch: Change file timestamps

ln: make a symbolic link for a directory.

Say you have a long source directory like /usr/local/source/file/compiler/bin/ and want to be able to see its contents more easily.

Try: ln -s /usr/local/source/file/compiler/bin/ easydir

to make a symbolic link in your existing directory as a subdirectory called “easydir”. To remove the symbolic link, just try “rm” per below.

df/quota: find out how much space is free for you to use.

On any filesystem, if you want to know how much free space there is,

Try: df -h

for human units (GB/MB/KB) to see how much space is free on all drives.

If your system has a quota set up (e.g. on a cluster for many users)

Try: quota -v

to find out if there’s a quota set up for you and how close you are to any existing limits.

cp/mv: copy or move files from one place to another. You may want to copy or move files around from one place to another. Here are some examples of copying or moving the old file apples.txt to oranges.txt.

Try: cp -i apples.txt oranges.txt

“i” for interactive means that if oranges.txt already exists, it will ask you if you want to overwrite.

Try: mv -i apples.txt oranges.txt

“i” for interactive means that if oranges.txt already exists, it will ask you if you want to overwrite the existing oranges.txt.

Try: mv -f apples.txt oranges.txt

“f” forces the move even if an existing oranges.txt is already there.

Try: cp -p apples.txt oranges.txt

“p” means that permissions and timestamps will be preserved.

Try: cp -r apples/ oranges/

“r” means that you’re recursively copying all the files in a directory. You need to do this if you’re trying to copy a directory.

rm: remove a file.

Much like cp and mv, you can remove files (be careful with this) using a couple different flags.

Try: rm -i apples.txt

to interactively ”i” remove a file (i.e. get a y/n statement)

Try: rm -v apples.txt

to get a verbose listing of the files removed.

Try: rm -r apples/

to recursively remove an entire directory.

chown/chmod: to change permissions of files.

Try: chown apples.txt

to make the an owner of the file apples.txt if it is not already the owner.

Try: chmod a+rw apples.txt

to make the file apples.txt readable and writeable by all. You can also rescind read or write access in the same way but using a ‘-’.

vi/nano/more/less: to edit or view a file.

Try: vi apples.txt

to open the files apple.txt with a text editor. Nano provides an easy text editing interface. And the other commands more/less can be used to view the file a page at a time but not to edit them. Check out these resources for viand nano for more info.

locate: check a database of indexed files

Try: locate apples

to find all paths and files that have the phrase apples somewhere in them. You can also use wildcards.

tar: compress and uncompress files.

Try: tar cvzf apples.tgz apples.txt

to create an archive of files. You can also use wildcards or a long list of files.

Try: tar zxvf apples.tgz

to expand an existing archive of files.

1. Getting connected:

Here are some useful tips for how to get started connecting to other machines.

ssh: secure shell remote login to a machine.

Try: ssh cardinal1.stanford.edu

to login to the machine cardinal1.stanford.edu. This will work if your username on the current computer is the same as the login for your destination.

Otherwise try: ssh -l usernew cardinal1.stanford.edu

Note: a handy trick is to alias common logins in your .bashrc or .profile (depending on what gets sourced when you open a new terminal).

As an example you could set an alias:

alias scard=”ssh -l usernew cardinal1.stanford.edu”

this would allow you to type scard to login rather than that whole long thing. Note you can use alias in your .bashrc/.profile to shorten all of your most common commands.

scp: secure copy

Try: scp -pr cardinal1.stanford.edu:/path/to/remotefile ./localfile

to secure copy a file from the cardinal1 filesystem to a local spot recursively and with preserved permissions and timestamps.

Try: scp -pr localfile cardinal1.stanford.edu:/path/to/

to secure copy a file from the local host to the cardinal1 filesystem.

sleep: sleep to keep the system waiting.

It may be useful to you to execute several commands and then sleep before executing more. Or you may find it useful to keep a connection alive to a server.

Try: sleep 5

to sleep at the command line for five seconds.

time: time how long it takes to execute a command.

Try: time to see how long it takes to execute a command.

ps: list the running processes

Try: ps aux

to see all the running processes.

kill: kill a process

Try: kill -9

to kill a process with one of the highest priorities.

wget: download a file from the web.

wget http://www.example.com/file.zip

3.Parsing data at the commandline.

It’s often useful to be able to manipulate data at the commandline. We’ll learn a few ways to do that here.

grep: find regular expressions

Try: grep ‘apple’ apples.txt

to see if the phrase ‘apple’ appears in apples.txt and how many times.

Try: grep -l ‘apple’ .

to return a list of files that have the phrase ‘apple’ in them.

awk: a more complicated regular expression tool.

Try: awk ‘/apple/ { print $2 }’ apples.txt

to return the 2nd record in any line that has the word ‘apple’ in it.

tail: get the tail of a file.

Starting from the bottom you can get the last N lines with ‘tail -N file’.

Try: tail -f myfile.txt

if you are running a program that is writing to myfile.txt, tail -f will update with the newly written lines from the file.

cat: show the file.

Try: cat myfile.txt

to cat all of the contents of the file to standard out.

Try: cat myfile.txt >> apples.txt

to add all the contents of myfile.txt to the end of apples.txt.

uniq: identify unique items in a list of items.

Try: cat apples.txt | uniq

to get all unique instances of lines in apples.txt. For instance if the word ‘apples’ appears twice on two separate lines, you’ll only get one result.

sort: sort items in a list.

Try: cat apples.txt | sort

to get everything sorted alphabetically.

Try: cat apples.txt | sort -n

to get everything sorted numerically.

Try: cat apples.txt | sort -rn

to reverse the numerical sort.

echo: send a phrase to standard out consisting of text or variables

You can specify a variable:

apples=”oranges”

And try using echo: echo $apples

the result will be: oranges

join : join lines of two files on a common field
Try: join FILE1 FILE2

wc: word count

Try: cat apples.txt | wc

to return the number of lines, words, and characters in the file.

Note: wc -l returns only the number of lines.

bc: calculator

Try: bc -l

to enter an interactive calculator to do math in.

Or try: echo “3+2” | bc

to add and return the resulting number to the standard out.

diff: identify line by line differences in a file.

Try: diff apples.txt oranges.txt

to get the line by line differences between two files.

sed: this line editor can allow you some useful ways to change lines in a file.

Say you want to get all of the lines from your file except those that start with ‘orange’.

Try: cat apples.txt | sed ‘/orange/d’ > applesnew.txt

where the ‘d’ stands for deleting all matching cases of that regular expression.

Variable Meaning in Shell

$0 Filename of script

$1 Positional parameter #1

$2 - $9 Positional parameters #2 - #9

${10} Positional parameter #10

$# Number of positional parameters

"$*" All the positional parameters (as a single word) *

"$@" All the positional parameters (as separate strings)

${#*} Number of positional parameters

${#@} Number of positional parameters

$? Return value

$$ Process ID (PID) of script

$- Flags passed to script (usingset)

$_ Last argument of previous command

$! Process ID (PID) of last job run in background