man
: manual page.
Explains how to use a shell command.
man <COMMAND>
: For example, to find out how to use man
, type man man
ls
: list directory content
cd
: change directory
pwd
: print working directory
wc
: count word, line, character, and byte
head
: display the first part of a file
default = 10 lines, change by -n
example: head -n 20 filename
(display the first 20 lines of filename
)
tail
: display the last part of a file
cat
: concatenate and print the file
more
: display output one screen at a time
cp
: copy file
mv
: move file (can be use as changing file name)
rm
: remove file (like delete)
chmod
: change file modes or Access Control Lists
(u,g,o): user, group, other
(r,w,x): read, write, execute
chown
: change file owner or group
mkdir
: make directories
rmdir
: remove directories
find
: search for files
examples:
find /PATH -type f -name “*.bam”
: find all files (-type f
) in /PATH
with the name *.bam
.
find /PATH -type d -name “flash”
: find all directories (-type d
) in /PATH
with the name flash
.
These examples are useful for calculating file sizes or clean up.
To calculate all file sizes, pipe the file names to xargs
and du
; find /PATH -type f -name “*.bam” | xargs du -csh
To remove all files found by the command, pipe the file names to xargs
and rm
; find ./ -type f -name “*.bam” | xargs rm
To remove all directories found by the command, pipe the directory names to xargs
and rm -r
; find ./ -type d -name “bwa_*” | xargs rm -r
ssh
: OpenSSH SSH client (remote login program)
scp
: secure copy (remote file copy program)
scp <SOURCE> USRNAME@IP:<DESTINATION>
scp USRNAME@IP:<SOURCE> <DESTINATION>
-p: 保留原始檔案權限&修改日期等, -r: 複製整個資料夾
2>&1
: send STDERR to STDOUT (0:STDIN, 1:STDOUT, 2:STDERR)
&
: running job in background (終端機背景執行)
nohup
: run a command in background; immune to hangups 系統背景執行
kill
: kill job
kill PID
: kill a job by the process id (PID)
ps -u USER | grep blast | cut -d ' ' -f 2 | xargs kill
: generate a list of all processes by USER, use grep
to find blast jobs, cut
out the PID, send to xargs
to kill the jobs.
free
: display amount of free and used memory in the system
grep
: find keywords in file
nice
and renice
: run a program with modified priority. If the server is under heavy load and you need to start a non-urgent large job, please use these.'
diff
:
wget
: download files