Get started

• Open terminal
 

 
• Download github repo (curl -L https://github.com/seb951/basic_unix/archive/master.zip >master.zip)
• Decompress it (unzip master.zip)
• It contains a few examples + .pdf version of tutorial

General principles

• All commands are short, perform simple tasks & are highly optimized (fast)
• Nearly all commands and options (~99%) work across Unix-based OS
• Commands can take (many) options
• Commands can be combined (see more later)
• Many commands don’t require any argument, some do
• command -option1 -option2 -optionN... parameter object
• Many commands output directly to terminal

Exploration

Command Meaning
ls what’s there
ls -1 with an option
ls -t -h with more options
ls -thor combining even more options
man ls how to run command (q = quit; d = next page; ; arrows & fn arrows = scrolling)
pwd where are we (full path)
cd move somewhere else (default to home)
cd .. move back
cd ../Applications move back, then forward
cd ~ move home
cd / move to root

Moving / removing / creating files

Command Meaning
mv move
cp copy
rm careful remove a file
rmdir careful remove an empty directory
rm -r VERY careful remove directory recursively
mkdir create empty directory
touch create empty file
echo print message to screen

Examining files

Command Meaning
head print first 10 lines to screen
tail print last 10 lines to screen
less print file line by line (use arrows + fn arrows to move up/down)
cat print file content to screen
sort sort a file
uniq unique lines in a file
clear clear terminal
wc wordcount
du disk usage

Tricks

Command Meaning
> redirect
>> append to file
| pipe
* anything (special character: for literal *, use \*)
? any character (special character)
Ctrl+A go to beginning of line in terminal
Ctrl+E end of line
tab key autocomplete

Working remotely

Command Meaning
ssh secure shell (remote connection)
scp secure copy (remote connection)

Other useful commands

Command Meaning
chmod change mode of file
sudo superuser do
top what’s running
kill kill a process
curl get stuff from web (MACOS native) or wget (MACOS non-native)
history see recent history (use ! with nb to use previous cmd)
open open a file
ln symbolic link
which where is a command
alias create own commands
nano edit text (whole file loaded in memory)
nano +123 specify location in file

Profile

• Let’s look at .bash_profile to modify options (e.g. nano ~/.bash_profile)
• Usefull options are here: examples/bash_example_commands

Compression

Command Meaning
gzip compression/decompression of files
gzip -cd file.gz decompress to standard out (use a > redirect)
gunzip compression/decompression of files
tar compression/decompression of archives
tar -xvzf file tar.gz decompress a tar.gz (tarball)

Regular expressions

Command Meaning
grep regular expression
grep -options 'pattern' file regular expression

Examples

Combining commands:

• Let’s look at the file examples/sequence.fasta
• print line 17 by piping head and tail
• Count lines starting with ‘>’ (pipe grep and wc)
• Count unique lines starting with ‘>’ (pipe grep, sort, uniq and wc)
• How many files is there in the directory (pipe ls & wc)

Install and run command line programs

• Let’s look at this example: https://github.com/rec3141/rec-genome-tools/blob/master/bin/fastagrep.pl
• Notice the !# (shebang) on the first line
• It is a short perl script that greps sequences in a .fasta formatted file
• Copy-paste the text in a new file (e.g. touch fastagrep.pl,nano fastagrep.pl, paste and save)
• Make it executable (chmod +x fastagrep.pl)
• Let’s look at it (./fastagrep.pl)
• Let’s try it (./fastagrep.pl 'deserticola' examples/sequence.fasta)
• Let’s symbolic link it so the computer knows where to find it (ln source target)

bash

• The terminal runs (by default) the bash command language
• We can write or use more complex executable bash code
• Let’s look at an example less examples/bash_cmd2