Linux Cheat Sheet

Linux/Unix Command Line Cheat Sheet - GettingGeneticsDone.blogspot.
com
Command
Description
pwd
prints working directory (prints to screen, ie displays the full path, or your location on the filesystem)
ls
lists contents of current directory
ls l
lists contents of current directory with extra details
ls /home/user/*.txt
lists all files in /home/user ending in .txt
cd
change directory to your home directory
cd ~
change directory to your home directory
cd /scratch/user
change directory to user on scratch
cd change directory to the last directory you were in before changing to wherever you are now
mkdir mydir
makes a directory called mydir
rmdir mydir
removes directory called mydir. mydir must be empty
touch myfile
creates a file called myfile. updates the timestamp on the file if it already exists, without modifying its contents
cp myfile myfile2
copies myfile to myfile2. if myfile2 exists, this will overwrite it!
rm myfile
removes file called myfile
rm f myfile
removes myfile without asking you for confirmation. useful if using wildcards to remove files ***
cp r dir newdir
copies the whole directory dir to newdir. r must be specified to copy directory contents recursively
rm rf mydir
this will delete directory mydir along with all its content without asking you for confirmation! ***
nano
opens a text editor. see ribbon at bottom for help. ^x means CTRL-x. this will exit nano
nano new.txt
opens nano editing a file called new.txt
cat new.txt
displays the contents of new.txt
more new.txt
displays the contents of new.txt screen by screen. spacebar to pagedown, q to quit
head new.txt
displays first 10 lines of new.txt
tail new.txt
displays last 10 lines of new.txt
tail f new.txt
displays the contents of a file as it grows, starting with the last 10 lines. ctrl-c to quit.
mv myfile newlocdir
moves myfile into the destination directory newlocdir
mv myfile newname
renames file to newname. if a file called newname exists, this will overwrite it!
mv dir subdir
moves the directory called dir to the directory called subdir
mv dir newdirname
renames directory dir to newdirname
top
displays all the processes running on the machine, and shows available resources
du h --max-depth=1
run this in your home directory to see how much space you are using. dont exceed 5GB
ssh servername
goes to a different server. this could be queso, brie, or provolone
grep pattern files
searches for the pattern in files, and displays lines in those files matching the pattern
date
shows the current date and time
anycommand > myfile
redirects the output of anycommand writing it to a file called myfile
date > timestamp
redirects the output of the date command to a file in the current directory called timestamp
anycommand >> myfile
appends the output of anycommand to a file called myfile
date >> timestamp
appends the current time and date to a file called timestamp. creates the file if it doesnt exist
command1 | command2
pipes the output of command1 to command2. the pipe is usually shift-backslash key
date | grep Tue
displays any line in the output of the date command that matches the pattern Tue. (is it Tuesday?)
tar -zxf archive.tgz
this will extract the contents of the archive called archive.tgz. kind of like unzipping a zipfile. ***
tar -zcf dir.tgz dir
this creates a compressed archive called dir.tgz that contains all the files and directory structure of dir
time anycommand
runs anycommand, timing how long it takes, and displays that time to the screen after completing anycommand
man anycommand
gives you help on anycommand
cal -y
free calendar, courtesy unix
CTRL-c
kills whatever process youre currently doing
CTRL-insert
copies selected text to the windows clipboard (n.b. see above, ctrl-c will kill whatever youre doing)
SHIFT-insert
pastes clipboard contents to terminal
*** = use with extreme caution! you can easily delete or overwrite important files with these.
Absolute vs relative paths.
Lets say you are here: /home/turnersd/scripts/. If you wanted to go to /home/turnersd/, you could type: cd /home/turnersd/. Or you could
use a relative path. cd .. (two periods) will take you one directory up to the parent directory of the current directory.
.
(a single period) means the current directory
..
(two periods) means the parent directory
~
means your home directory
A few examples
mv myfile ..
cp myfile ../newname
cp /home/turnersd/scripts/bstrap.pl .
cp myfile ~/subdir/newname
more ../../../myfile
moves myfile to the parent directory

copies myfile to the parent directory and names the copy newname
copies bstrap.pl to . i.e. to dot, or the current directory youre in
copies myfile to subdir in your home, naming the copy newname
displays screen by screen the content of myfile, which exists 3 directories up
Wildcards (use carefully, especially with rm)

*
matches any character. example: ls *.pl lists any file ending with .pl ; rm dataset* will remove all files beginning with dataset
[xyz] matches any character in the brackets (x, y, or z). example: cat do[or]m.txt will display the contents of either doom.txt or dorm.txt

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Linux/Unix Command Line Cheat Sheet - GettingGeneticsDone.blogspot.

moves myfile to the parent directory

Wildcards (use carefully, especially with rm)

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