• Unix course – Introduction to basic Unix commands
  • List of commands
  • Tutorial
    • Part 1
      • 01 - Accessing SimpleVM
      • 02 - Opening a terminal window
      • 03 - Creating a directory to work in
      • 04 - Running a simple program
      • 05 - Running in background and saving output
      • 06 - Inspecting and terminating a running program
    • Part 2
      • 07 - Extracting data from text files
      • 08 - Processing the extracted data
      • 09 - Downloading and compressing files
      • 10 - Cleaning up
    • Part 3: Advanced Concepts
      • 11 - Edit files
  • Questions and discussion
  • Remarks for the presenter

On Unix, every user has a unique user name. When they log onto the system, they are placed in a home directory, which is a portion of the disk space reserved just for them. When you log onto a Unix system, your main interface to the system is called the Unix Shell. This is the program that presents you with the dollar sign ($) prompt. This prompt means that the shell is ready to accept your typed commands. It is often preceded by the user name as well as the current directory.

Unix commands are strings of characters typed in at the keyboard. To run a command, you just type it in and press the Enter key. We will look at several of the most common commands below. Commands often have parameters, e. g. a file to work on. Theses are typed in after the command and are separated by spaces, e. g. less pi_results.txt opens the file pi_results.txt for reading.

In addition, Unix extends the power of commands by using special flags or switches. Switches are usually preceded with a dash (-), e. g. ls -lh.

Download as PDF or separate MarkDown.

During this tutorial you will use many of the commands above. Your task is to identify the correct commands and execute them. Feel free to experiment. Take a look at the solution if absolutely necessary.

This tutorial is based on the tutorial that was created by the de.NBI Cloud Bielefeld administrators. The first two sections (01 and 02) describe how to access the CLUM 2021 environment for this tutorial. Participants need a web browser and an active ELIXIR account.

When accessing a Unix system running as a virtual machine in the cloud one would normally log into it via SSH and would be getting presented with a terminal. For the sake of this tutorial the access route to the terminal is via web browser. Every participant has access to a prepared virtual machine running a web-based development environment called Theia IDE.

Accessing Theia IDE

This workshop is powered by SimpleVM. Every participant should have received a mail containing the actual link to their VM. If you did not receive a mail containing a link to a VM, please contact your tutor.

After successful login the Theia IDE screen appears. The screen is usually divided into 3 sections: Editor pane in the center, file browser on the left, terminal at the bottom. This tutorial will primarily focus on the use of the terminal.

Note: Access to your own private virtual machine works different from what is used here. You would usually run an SSH client to connect to the machine using a key file and would then be presented with a single terminal command prompt, e.g.: ssh -i ~/.ssh/mykeyfile [email protected]

If not yet open go to -> Terminal -> new Terminal to open a new terminal.

It is possible to have more than one terminal open at the same time.

Tasks:

1. Open the manual page of the command pwd by entering man pwd.
2. Find out your current (working) directory. (1 command)
3. If your current directory is not your home directory, please move to it. (1 command)
4. Now create a directory called pi_calculation and enter the new directory. (2 commands)
5. Confirm that your current directory has changed. (1 command)

pwd
cd ~
mkdir pi_calculation
cd pi_calculation
pwd

A simple program that (slowly) approximates the number pi is available as a file at /opt/calculate_pi.

Tasks:

1. Please copy this program into your current directory. (1 command)
2. Inspect the file you just copied to get information about its file type. (1 command)
3. Please make the file executable (for you as the owner only). (1 command)
4. Now run the executable and watch how the pi approximation gets better over time. (1 command)
5. Stop the running program by pressing the key combination Ctrl+c.

cp /opt/calculate_pi .
file calculate_pi
chmod u+x calculate_pi
./calculate_pi

We would like to save the results of the pi calculation program to a file instead of just displaying them on the screen.

Tasks:

1. Please run the pi executable again but this time send its output to a file called pi_results.txt in the same directory. (1 command)
2. Open a second terminal and enter a command that allows you to watch the output lines being written to the results file. Note: Bear in mind that a new terminal always starts in your home directory. (2 commands)
3. Stop following the results file. (1 key combination)

./calculate_pi > pi_results.txt
cd pi_calculation
tail -f pi_results.txt
# Ctrl+c

The pi approximation will probably run for about an hour but we would like to terminate it earlier.

Tasks:

1. List your own running programs. (1 command)
2. Use the process ID (PID) of the still running pi calculation to terminate it. The PID is in the first column of the program list. (1 command)
3. Verify that the pi calculation has stopped. (1 command or action)
4. Inspect the contents of the results file that the pi calculation has generated. (1 command)
5. Check the file size of the results file. (1 command)
6. Check the free disk space available in the current directory. (1 command)

ps -x
kill 
ps -x     # or look at the first terminal
less pi_results.txt
ls -lh
df -h .

Let's extract adverbs from a list of English words available inside /usr/share/dict/words.

Tasks:

1. Please move to your home directory. (1 command)

2. Now create a directory called fun_with_words and enter the new directory. (2 commands)

3. Filter the English words list for words ending in …fully and save them to a file named fully.txt using the command below. The $ sign inside the search string ensures that only word endings are matched.

   grep "fully$" /usr/share/dict/words > fully.txt
   
   

4. Take a look at the contents of fully.txt. (1 command)

5. Repeat the same for the words ending in …ously as well as …ably and save them to their corresponding files. (2 commands)

6. Calculate the word counts of all three files. (1 command)

cd ~
mkdir fun_with_words
cd fun_with_words
grep "fully$" /usr/share/dict/words > fully.txt
less fully.txt
grep "ously$" /usr/share/dict/words > ously.txt
grep "ably$" /usr/share/dict/words > ably.txt
wc ably.txt fully.txt ously.txt

1. Convert all the adverbs inside the three files from the previous section into adjectives. Name the resulting files able.txt, ful.txt and ous.txt (3 commands)

   adverb	adjective
   …ably	…able
   …fully	…ful
   …ously	…ous

2. Concatenate the contents of able.txt, ful.txt and ous.txt into a single file called adjectives.sorted.txt. Sort the lines alphabetically before saving. (2 commands with a pipe in between)

3. Take a look at the results. (1 command)

sed 's/ably/able/' ably.txt > able.txt
sed 's/fully/ful/' fully.txt > ful.txt
sed 's/ously/ous/' ously.txt > ous.txt
cat able.txt ful.txt ous.txt | sort > adjectives.sorted.txt
less adjectives.sorted.txt

1. Please move to your home directory. (1 command)
2. Now, download the file at https://tinyurl.com/sars-cov-2-seq to the current directory using a network downloader. (1 command)
3. Take a look at the contents of the file. (1 command)
4. The downloaded file is an uncompressed text file of 30 Kilobytes in size. Please apply compression to the file so that it takes less disk space and check the effectiveness of the compression. (2 commands)

cd ~
wget "https://tinyurl.com/sars-cov-2-seq"
less sars-cov-2-seq
gzip sars-cov-2-seq
ls -l sars-cov-2-seq.gz

1. Please enter your home and list its contents. (2 commands)
2. Please list the contents of the directory fun_with_words without moving into it. (1 command)
3. Now, delete all the files inside the directory fun_with_words. (1 command)
4. Delete the directory itself. (1 command)
5. The directory pi_calculation has to be cleaned up as well. This time, delete directory and contents in one go. (1 command)
6. Verify that both directories have been removed. (1 command)
7. Remove the compressed text file. (1 command)
8. That's it! Congratulations! You have mastered the Unix command-line essentials!

cd ~
ls
ls fun_with_words
rm fun_with_words/*
rmdir fun_with_words
rm -r pi_calculation
ls
rm sars-cov-2-seq.gz

Instead of using a graphical user interface for editing files, you can directly manipulate files on the terminal.

1. Please move to your home directory. (1 command)
2. Download the sars-cov-2 genome again (https://tinyurl.com/sars-cov-2-seq). (1 command)
3. Open the file in an editor. (1 command)
4. Remove all characters from the first line with the exception of the fasta id (>NC_045512.2). (typing/removing text)
5. Save the file and exit the editor. (1 key combination and 2 keys)
6. Output just the first 10 lines to ensure that the fasta header contains only the id now. (1 command)

cd ~
wget "https://tinyurl.com/sars-cov-2-seq"
nano sars-cov-2-seq
# Moving the caret and pressing backspace to remove the characters
# Ctrl+x, then type y to save the buffer and press enter to confirm the filename
head sars-cov-2-seq

If something is unclear or if you have further questions, do not hesitate to ask us.

Please make sure that

• /opt/calculate_pi is in place and not executable
• the Ubuntu package wamerican-small is installed