UNIX Commands
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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
