Cheatsheet for UofABioinformaticsHub Introduction to BASH Workshop

Navigation and file management

Command/Symbol	Description	Useful options	Section
man	Display on-line manual	-k
pwd	Print working directory, i.e show where you are	none commonly used
ls	List contents of a directory	-a, -h, -l
cd	Change directory	(scroll down in man builtins to find cd)
mv		-b, -f, -u
cp		-b, -f, -u
rm		-r (careful…)
rmdir
mkdir		-p

File viewing

Command/Symbol	Description	Useful options	Section
cat
less
more
head		-n# (e.g., -n100)
tail		-n# (e.g., -n100)
wc		-l

Keyboard shortcuts

Command/Symbol	Description	Useful options	Section
[Tab]	tab-autocomplete
[Up]/[Down]	Cycle through previous commands
[Ctrl][Shift]-C, [Ctrl][Shift]-V	Copy and paste highlighted text in terminal

Filters, file/stream editing

Command/Symbol	Description	Useful options	Section
cut		-d, -f, -s
paste
sort
uniq		-c
grep
echo		-e
tee
sed
awk

General utilities

Command/Symbol	Description	Useful options	Section
history		-c
top
ps		-u
kill, pkill		-u
whoami		-u
fg	bring process to foreground

Network

Command/Symbol	Description	Useful options	Section
wget
curl

Special symbols

Command/Symbol	Description	Useful options	Section
|
>, >>
<
&
*, ?	wildcards
\

Archiving and compression

Command/Symbol	Description	Useful options	Section
tar		-x -z -c -v -f
gunzip, gzip		-k, -c