UNIX Commands

Shorthand Key:

file name		flnm
database name		dbnm
table name		tblnm

Common Unix Commands

pwd				present working directory
ls				list directories/files
ls –ltr				lists directories/files without a “.” in front
ls –ltra			lists directories/files with a “.” In front
ls -1				lists directories/files with one entry on each line
ls –L				shows just sym link names, not destination
ls –L1 flnm*			shows names & sym links & lists them one/line that start with “flnm”
!$				last argument on previous line (space to end)
hgsql dbnm		        gets us in mysql database
Ctrl + c			cancels command in progress
h				history
cp				copy
mkdir				make directory
cd -				back to the last place you were
cd				takes all the way to the top no mater where you are
grep				search/find
egrep				extended grep
-v				remove this
rm flnm				remove file
diff flnm1 flnm2		shows differences between two files
cp flnm				copy file
mv flnm				move copy file
mv flnm1 flnm2		        rename file from flnm1 to flnm2 (overwriting flnm2 if it already existed)
^				beginning of a line or begins with
\				escapes a character (insert char. don’t execute its comnd)
|				pipe to
df				name of machine
command | more		        give the first few records & give one more line when "enter" is clicked
> flnm			        put in file
J				takes next line and prints it to the screen
:. , $				from here to the end of the line
~				toggles between the last two places
ssh machine		        open shell on that machine (ex  ssh hgwdev)
cat flnm			print this file to the screen (rather than vi)
cat flnm | grep “criteria”	print only the criteria of the file to the screen
head flnm			first 10 lines of file in window
tail flnm			last 10 lines of file in window
history				shows you every command typed in session
!#				displays that line number in command line (ex. !20)
sudo mypush db tbl hgwbeta	push a table to hgwbeta (from dev)
diff flnm1 flnm2		difference between two files

cat flnm | awk -F\. '{ print $1 }'	makes deliminator a "." and prints the first column (before the ".")

ls -1 | wc -l 			number of flies in a directory
ps				processes running in terminal, -e for everything, -ef for everything full, | grep katrina for just my stuff
ctrl+z				halts a job
bg				background (must do ctrl+z first)
fg				foreground
top				display processes currently running in real time (default sort is by highest CPU usage)
uptime				displays how long the system has been up (without reboot) and recent overall CPU usage
man cmd1			show the manual page for the command cmd1 (this is for unix commands, not programs we write)

samtools view -x <file> <pos> | grep <QNAME> | sed 's/\t/\n/g'		prints bam records in a region with particular QNAME vertically with the FLAG field in hex (made alias: sv = 'samtools view -x')

To view processes: http://www.cyberciti.biz/faq/show-all-running-processes-in-linux/
kill processId		to force quit a command that you can't "ctrl + c" out of (must open another window and view processes first)

Sym Link

• Make a Sym Link:

ln –s location sym link name

ex.
ln –s kent/src/hg/makeDb/trackDb trackDb

• Use a Sym Link:

cd ~/sym link name

ex.
cd ~/trackDb

Resources

• Unix Tutorial: http://www.ee.surrey.ac.uk/Teaching/Unix/
• Parts I and II of this tutorial: http://korflab.ucdavis.edu/Unix_and_Perl/current.html
• This free PDF download about the Linux Command line, http://linuxcommand.org/tlcl.php, has more in-depth information where chapters 1–7, 9, 11, 18, 19, 20, and maybe 24–33 have been recommended.
• Recommended paper on The UNIX Time-Sharing System