| Command | Translation | Examples |
|---|---|---|
cd |
change directory | cd /absolute/path/of/the/directory/ Go to the home directory by typing simply cd or cd ~ Go up (back) a directory by typing cd .. |
pwd |
print working directory | pwd |
mkdir |
make directory | mkdir newDirectory creates newDirectory in your current directory Make a directory one level up with mkdir ../newDirectory |
cp |
copy | cp file.txt newfile.txt (and file.txt will still exist!) |
mv |
move | mv file.txt newfile.txt (but file.txt will no longer exist!) |
rm |
remove | rm file.txt removes file.txt rm -r directoryname/ removes the directory and all files within |
ls |
list | ls *.txt lists all .txt files in current directory ls -a lists all files including hidden ones in the current directory ls -l lists all files in current directory including file sizes and timestamps ls -lh does the same but changes file size format to be human-readable ls ../ lists files in the directory above the current one ls -lrS lists files sorted by size in reverse ls -lt lists files sorted by time ls -lx lists files sorted by file extension |
man |
manual | man ls opens the manual for command ls (use q to escape page) |
grep |
global regular expression parser |
grep ">" seqs.fasta pulls out all sequence names in a fasta file grep -c ">" seqs.fasta counts the number of those sequences |
cat |
concatenate | cat seqs.fasta prints the contents of seqs.fasta to the screen (ie stdout) |
head |
head | head seqs.fasta prints the first 10 lines of the file head -n 3 seqs.fasta prints first 3 lines |
tail |
tail | tail seqs.fasta prints the last 10 lines of the file tail -n 3 seqs.fasta prints last 3 lines |
wc |
word count | wc filename.txt shows the number of new lines, number of words, and number of characters wc -l filename.txt shows only the number of new lines wc -c filename.txt shows only the number of characters |
sort |
sort | sort filename.txt sorts file and prints output |
uniq |
unique | uniq -u filename.txt shows only unique elements of a list (must use sort command first to cluster repeats) |
| Shortcut | Use |
|---|---|
| Ctrl + C | kills current process |
| Ctrl + L | clears screen |
| Ctrl + A | Go to the beginning of the line |
| Ctrl + E | Go to the end of the line |
| Ctrl + U | Clears the line before the cursor position |
| Ctrl + K | Clear the line after the cursor |
* |
wildcard character |
| tab | completes word |
| Up Arrow | call last command |
. |
current directory |
.. |
one level up |
~ |
home |
> |
redirects stdout to a file, overwriting file if it already exists |
>> |
redirects stdout to a file, appending to the end of file if it already exists |
| ` | ` |