Introduction to Unix 1

General information

Topic overview

In this lesson you will learn about Unix: an operating system that runs on almost all high performance computing (HPC) servers, which we interface with via the command line.

Learning objectives

Learning Objective 1 - You understand the inner workings of the computer: how files are organized and how processes are run

  • You execute commands on the command line

  • You navigate the file system using commands

  • You create, modify, move, copy files and directories

Learning Objective 2 - You recognize the difference between local and remote servers and are able to communicate within and between them

  • You transfer files back and forth between your local computer and the remote server

What is Unix?

Unix is a family of operating systems - sets of programs that manage the use of computer hardware resources by software applications. It thereby allows multiple users to access a computer simultaneously, perform parallelized computations, exchange data and share hardware resources. This diagram shows an oversimplified view of an operating system - the kernel (in blue) is a core program that is always active and controls interactions between the hardware (in green), and software (in red).

Technically, our servers use a version of Linux, a Unix-like operating system. Furthermore, even major operating systems such as Android and MacOS are Unix-based underneath.

The command

Commands are our tool to tell the computer what to do. Most commands have options and arguments. Arguments are often essential for a command to operate properly; they are the pieces of information required by a command, such as a file name. Options are, of course, optional, and offer ways to modify the way the command works.

For instance, echo will take any text you give it as an argument and then send it back to you as output:

# My first command
echo 'Hello World!'

If you use the option -n, then it will not add a ‘new line’ to the end of the output:

# My second command
echo -n 'Hello World!'

Some commands end up with very complex structures, because they can have many options and arguments. In general, options will be of the format -a where a is a single letter or --word where word is a string (a series of letters, in computer terms).

Note: the command line is case-sensitive! So it does matter if you write -a or -A.

Getting help

The man command will show a manual for most basic commands, providing the correct syntax to use it and the various options available.

# Read the manual
man ls

Other programs have different ways to provide help on how to use them. An online tutorial is best, or a comprehensive manual, but sometimes you only have the command line to help you.

# Help please!
python3 -h
python3 --help

Useful command line tricks

  • You can use the up and down arrow keys to navigate through previously used commands (known as your history) and repeat or modify them.

  • Windows: To copy text from the terminal you will have to highlight it and right-click to use the in-browser menu and copy. Similarly you have to use the in-browser menu to paste into the terminal. The reason for this is that Ctrl + c and Ctrl + v have effects inside the terminal.

  • Mac: You can fortunately use Cmd + c and Cmd + v to copy and paste as normal. You can use Ctrl and various keys for in-terminal commands.

  • When typing a command or file name, you can press the ‘tab’ key to auto complete what you are typing. If there are multiple commands or files with similar names, auto completion will fill in as far as the first ambiguous character before you have to give it some more input. This method makes it much less likely that you make a spelling error. Also, if you double press the ‘tab’ key all the available options to complete will be shown.

  • Pressing Ctrl + c will send an interrupt signal that cancels the currently running command and brings you back to the command line.

  • Pressing Ctrl + r will allow you to search through your command history.

  • Pressing Ctrl + l will clear the screen.

  • See previous commands by typing history and pressing enter.

  • Double-click to select a word, triple-click to select a line

  • Using a # character allows you to make comments that have no effect when run.

Exercise 1.1

  • Try to echo “My first command”

#echoing "My first command"
echo 'My first command'

  • Use the arrow key to execute the same command again

 # Press the up arrow once and the last command appears
echo 'My first command'

  • Try typing e then pressing tab twice, what do you see?

# You see all the possible commands that start with "e" when you press tab twice after entering “e”
e2freefrag             edquota                era_check              eu-readelf
e2fsck                 efibootdump            era_dump               eu-size
e2image                efibootmgr             era_invalidate         eu-stack
e2label                efikeygen              era_restore            eu-strings
e2mmpstatus            efisiglist             esac                   eu-strip
e2undo                 efivar                 escputil               eutp
e4crypt                egrep                  espdiff                eu-unstrip
e4defrag               eject                  espeak-ng              eval
eapol_test             elfedit                ether-wake             evince
easy_install-2         elif                   ethtool                evince-previewer
easy_install-2.7       else                   eu-addr2line           evince-thumbnailer
easy_install-3         enable                 eu-ar                  evmctl
easy_install-3.6       encguess               eu-elfclassify         ex
ebtables               enchant-2              eu-elfcmp              exec
ebtables-restore       enchant-lsmod-2        eu-elfcompress         exempi
ebtables-save          enscript               eu-elflint             exit
echo                   env                    eu-findtextrel         exiv2
ed                     envsubst               eu-make-debug-archive  expand
edgepaint              eog                    eu-nm                  export
edid-decode            eps2eps                eu-objdump             exportfs
editdiff               eqn                    eu-ranlib              expr

  • Try adding c to make ec and pressing tab again. What happens?

# The command autocompletes after adding the “c” to the “e”
echo

  • Try to copy/paste your echo command “echo ‘My first command’”

# Note that ctrl + c to copy does not work in windows terminal or mobaxterm - instead highlighting text automatically copies it
# In mobaxterm ctrl + v to paste also does not work - instead right-click to paste
echo 'My first command'

  • Try to clear the screen, can you still paste your echo command?

# To clear the screen use ctrl + l or the command 'clear' and you can still paste the command
echo 'My first command'

  • Try to echo ‘My first command ‘once with the -n option and once with the -N option. What do you notice?

# echo -n does not add a new line to the output
echo -n 'My first command'
My first command[]$

# The -N option does not exist therefore “echo” will ill interpret '-N' as characters to display
echo -N 'My first command'
-N My first command

  • Try to look at the manuel of the echo command.

# man gives you the manual of the function
man echo

The file system

You may be used to the file system in Windows or Mac OS X, where directories (or folders if you prefer) can contain files and more directories. The Unix filesystem is structured in the same way - as a tree - that begins at the ‘root’ directory ‘/’. Directories are separated by slash characters /.

Click on the image below to see what your file system could look like. In this example the root directory is dir1.

When you work on the command line, you are located in a directory somewhere in this tree. There are two ways to refer to a location: its absolute path, starting at the root directory, or its relative path, starting in the current directory.

# Absolute path
/nfs/course/home/<user_name>

# Relative path
../../home/<user_name>

The .. refers to the directory above a location, so the relative path here goes up twice, then back down to your home directory. If a path starts with ~/ then it refers to your home directory. If a path starts with ./ then it refers to the current directory.

# References the level above
../

# References the home directory
~/

# References the current directory
./

Wildcards

When providing a file path as an argument to a command, it is often possible to provide multiple file paths using wildcards. These are special characters or strings that can be substituted for a matching pattern. For many commands using wildcards allows you to execute the associated action on each file that matches the pattern, though this obviously does not work in all cases.

  • ? matches any single character

  • * matches any number of any characters

  • […] matches any character within the brackets

  • {word1,word2,…} matches any string inside the brackets

For instance:

# Pattern matching
ls /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/*      # lists all files in the ecoli directory
ls /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/*.fna  # lists all nucleotide fasta files there
ls /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/*.f?a  # lists all nucleotide and protein fasta files there

Basic file operations

cp copies a file from one location to another. The example will copy a file containing the genome sequence of E. coli K12 MG1655 to your home directory.

# Copy
cp <source> <destination>
cp /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna ~/

mv moves a file from one location to another. The example actually renames the file, because the destination is not a directory. Thus you can move and rename a file with the same command.

# Move or rename
mv <source> <destination>
mv ~/GCF_000005845.2_ASM584v2_genomic.fna ~/E.coli_K12_MG1655.fna

rm removes a file, so use it with care.

# Remove
rm <path_to_file>
rm ~/E.coli_K12_MG1655.fna

mkdir creates a new directory with the given name.

# Make directory
mkdir <path to directory>
mkdir genomes

rmdir removes an empty directory.

# Remove an empty directory
rmdir <path to directory>
rmdir genomes

Click on the image below to see what every command will do within your file system.

Exercise 1.3

  • Create three new directories called “genomes”, “test” and “in_class” in your home folder

# First go to your home folder
cd
# Use the mkdir function to create a directory
mkdir genomes
mkdir test
mkdir in_class

  • Delete the test directory

# Use the rmdir function to remove a directory
rmdir test

  • Copy the /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna file into your new directory “genomes”

# Use the cp function to copy. cp <source> <destination>
cp /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna ~/genomes

  • Rename the file to “E.coli_K12_MG1655.fna”

# Use the move function to rename a file mv <source> <destination>
# Enter the genomes directory
cd genomes
# Rename file
mv GCF_000005845.2_ASM584v2_genomic.fna E.coli_K12_MG1655.fna

  • Use the help option of the ls function to find out which option will give file size in a human-readable format. Remember that ls -l will give a table of file information including size.

# ls -l will give you a table of information but the file sizes are long and hard to read
ls -l

# ls --help lists all the options possible
ls --help

# The -h option makes file sizes human-readable, however file sizes are only printed when you use the -l flag so you must use both
ls -l -h
ls -lh
# The size should be 4.5M

  • Using man and cp, find out how to copy a directory.

# Enter home directory
cd
# Create two directory
mkdir dir1
mkdir dir2

# Try to copy dir1 into dir2
cp dir1 dir2
cp: dir1 is a directory (not copied).

# If you check 'man cp', you see that you have to use -R:
man cp
cp -R dir1 dir2

# Check if the directory has been copied
ls dir2

File name conventions

In Unix systems there are only really two types of files: text or binary. The file name ending (.txt or .jpg) doesn’t really matter like it does in Windows or Mac OS, however it is used to indicate the file type by convention. Some file types you will encounter include:

  • .txt - A generic text file.

  • .csv - A ‘comma separated values’ file, which is usually a table of data with each line a row and each column separated by a comma.

  • .tsv - A ‘tab separated values’ file, which is the same but separated by tab characters.

  • .fasta or .fa - A fasta formatted sequence file, in which each sequence has a header line starting with ‘>’.

  • .fna - A fasta formatted nucleotide sequence file, usually gene sequences.

  • .faa - A fasta formatted protein sequence file.

  • .sh - A ‘shell script’, which contains commands to run.

  • .r - An R script, which contains R commands to run.

  • .py - A python script, which contains python commands to run.

  • .gz or .tar.gz - A file that has been compressed using a protocol called ‘gzip’ so that it takes up less space on the disk and transfers over the internet faster.

Other useful file operations

Transferring files between computers

There are many different protocols for transferring files between computers. You may have heard of FTP - File Transfer Protocol - which is a non-secure but commonly used example. A more secure file transfer protocol is SCP - Secure Copy Protocol, and programs such as WinSCP use it. The command scp is an easy way to transfer a file immediately between the server you are working on and another (or two different servers!). Another command to copy files is rsync, which can be used with many options such as preserving the ownership and date of creation of a file (and much more).

Be aware that all the scp commands shown below have to be executed on your local computer. Thus if you are currently connected to a server, you first have to exit this connection to be connected to your local computer again (Windows Command or Mac Terminal).

Tip: Remember that with the ‘tab ‘ key you can auto complete and see the available options by double pressing. This can make finding a file you want to upload way easier. (Note: This works only for the machine you are currently on.)

# Secure CoPy
man scp
scp /path/to/source user@server:/path/to/destination # local server (where the command is executed) to remote server
scp <user>@server:/path/to/source /path/to/destination # remote server to local
scp <user>@server1:/path/to/source <user>@server2:/path/to/destination # remote server 1 to remote server 2

# Download an E. coli genome from the server to your local computer
# First open Windows Command or Mac Terminal on your local computer
scp <user>@cousteau.ethz.ch:/nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna .
# Note that the local path is just "." - this means "here", i.e.: your working directory

# Copy the E.coli genome (or any file) from your local computer to the home folder on the server
# Again, on your local system, run the following commands in Windows Command or Mac Terminal
scp GCF_000005845.2_ASM584v2_genomic.fna <user>@cousteau.ethz.ch:~/

# Copy the E.coli genome from cousteau to euler, executed on cousteau
scp GCF_000005845.2_ASM584v2_genomic.fna <user>@euler.eth.ch:~/

# Copy the E.coli genome from cousteau to euler, executed on your own computer
scp <user>@cousteau.ethz.ch:GCF_000005845.2_ASM584v2_genomic.fna <user>@euler.ethz.ch:~/

Warning

Windows Paths

Windows terminal is not unix-like - instead it is based on MS-DOS and uses some different commands and conventions. Paths on Windows terminal use backslashes instead of forward slashes, and the root is the letter assigned to the drive where the path is. For instance a file in my downloads folder might have the path:

C:\Users\fieldc\Downloads\file.txt

Sometimes you want to download a file directly from the internet to the server, rather than going via your local machine. For using this command, you have to connect to the server first and then wget allows you to download files in this way.

# Download from the internet
wget source-URL
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/482/265/GCF_000482265.1_EC_K12_MG1655_Broad_SNP/GCF_000482265.1_EC_K12_MG1655_Broad_SNP_genomic.fna.gz

Compressing and decompressing files

Files can be compressed to take up less space on the hard drive (disk), or for transfer over the internet. The file you downloaded is an example, and we can decompress it using the gunzip command:

# Decompress a file
gunzip GCF_000482265.1_EC_K12_MG1655_Broad_SNP_genomic.fna.gz

If you ever need to compress a file, for instance to send it to someone, you can use the gzip command:

# Compress a file
gzip GCF_000482265.1_EC_K12_MG1655_Broad_SNP_genomic.fna

Exercise 1.4

  • Download the mystery image /nfs/teaching/551-0132-00L/1_Unix1/mystery_image.jpg from the server to your local machine. What is it?

scp <your eth name>@cousteau.ethz.ch:/nfs/teaching/551-0132-00L/1_Unix1/mystery_image.jpg .

A cat

  • On the server, download the E. coli file from the example above to your home folder.

# Make sure I am in my home directory
cd ~

# Download the file
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/482/265/GCF_000482265.1_EC_K12_MG1655_Broad_SNP/GCF_000482265.1_EC_K12_MG1655_Broad_SNP_genomic.fna.gz

  • Decompress the file.

#Decompress it
gunzip GCF_000482265.1_EC_K12_MG1655_Broad_SNP_genomic.fna.gz

Working with files

Looking at files

The command cat displays the entire contents of a file directly on the terminal. For large files this can be disastrous, so remember that you can cancel commands in progress with ctrl + c.

# ConCATenate
cat E.coli_K12_MG1655.fna

The command head displays only the first 10 lines of a file directly on the terminal. If you look at the available options for the command, -n x outputs the first x lines instead, and using a negative number outputs the lines except for the last x.

# Show file head
head E.coli_K12_MG1655.fna
head -n 1 E.coli_K12_MG1655.fna

The command tail displays only the last 10 lines of a file directly on the terminal. It has similar options to head; -n x outputs the last x lines, and using a positive number +x (note the “+” character) outputs the lines except for the first x.

# Show file tail
tail E.coli_K12_MG1655.fna

The command less is a versatile way to look at a file in the command line. Instead of showing you the contents of a file directly on the terminal, it ‘opens’ the file to browse. You can use the arrow keys, page up, page down, home, end and the spacebar to navigate the file. Pressing q will quit. A number of useful options exist for the command, such as showing line numbers or displaying without line wrapping. It also has a search feature that we will cover later.

# Browse file
less E.coli_K12_MG1655.fna

The command wc is a command that will quickly count the number of lines, words and characters in a file, including invisible characters like ‘newline’ and whitespace. Its options allow you to specify which value to return, otherwise it gives all three.

# Count things
wc E.coli_K12_MG1655.fna

Exercise 1.5

  • Use cat to look at the E. coli genome file you copied last time, is it suitable for looking at this file?

# Your file should be located in your genomes directory
cd ~/genomes/

# If you have not copied and renamed the file yet, you can use these commands to do so
cp /nfs/teaching/551-0132-00L/1_Unix1/genomes/bacteria/escherichia/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna ~/genomes
cd ~/genomes
mv GCF_000005845.2_ASM584v2_genomic.fna E.coli_K12_MG1655.fna

# Looking at the file
cat E.coli_K12_MG1655.fna
# Press ctrl + c to cancel the command

  • Use head and tail to examine the first and last 10 lines of the genome file. Now try to look at the first and last 20 lines.

# Look at the first 10 lines (10 is the default value)
head E.coli_K12_MG1655.fna

# Look at the last 10 lines
tail E.coli_K12_MG1655.fna

# Look at the first 20 lines
head -n 20 E.coli_K12_MG1655.fna

# Look at the last 20 lines
tail -n 20 E.coli_K12_MG1655.fna

  • Use less to look at the genome file. Navigate through the file with the keys listed above, then return to the Terminal.

# Looking at the genome file
less E.coli_K12_MG1655.fna
#press q to quit

  • Use the man command we learned to read about the wc command.

# Read about the wc command
man wc

  • Can you find out how many lines are in the genome file with the wc command?

# Count the number of lines in the file
wc -l E.coli_K12_MG1655.fna

In-class problems

What are In-class Problems?

  • During the week between classes, you will be expected to work through the Online Learning Material (OLM) provided on these web pages to learn the relevant material for the coming class.

  • In class, we will take time to answer any questions you may have and then work on more advanced problems together, which you can find at the end of each section of the OLM.

  • The problems relating to this section can be found at the end of the next section, Unix 2, as we will cover both sections in the same class in week 2.

Next: Introduction to Unix 2