Basic Unix for Biologists is aiming to helps anyone who would like to learn basic unix programming. This introduction/tutorial dose not require installation, you can simply click you can simply use Rstudio Cloud on your browser. Basic Unix for Biologists (EP1) will show you how this tutorial is setup and also introduce you to unix shell programming which will prepare you for Basic Unix for Biologists (EP2.)
เว็บเพจนี้สอน Unix Shell เบื้องต้น โดยผู้เรียนไม่ต้องดาวน์โหลดโปรแกรมลงบนคอมพิวเตอร์ส่วนตัว เพียงใช้ Rstudio Cloud บนเว็บบราวเชอร์ Basic Unix for Biologists (ตอนที่ 1) จะเริ่มต้นกล่าวถึงองค์ประกอบของข้อมูลที่จะใช้ในการเรียน Basic Unix for Biologists และแนะนำเกี่ยวกับ Unix Shell เบื้องต้น เพื่อเตรียมความพร้อมสำหรับ Basic Unix for Biologists (ตอนที่ 2)
Open Binder and Launch Terminal
Step A: Open Rstudio cloud and Launch Terminal
Once you log in to Rstudio cloud, your web browser should bring up a similar window as the picture shown above. Click the button on the top right corner to create a new Rstudio project. Then, the next step is to click “Terminal” which should look like a picture below after you click on it.
Download example files
/cloud/project$ svn export https://github.com/NatPombubpa/Binder_Intro_Unix/trunk/unix_intro
/cloud/project$ svn export https://github.com/NatPombubpa/Binder_Intro_Unix/trunk/data-shell
If everything work perfectly for you, you are ready for the tutorial.
What can a computer do simple term?
Naigate files, run programs/applications, store data, interact with users etc.
- Graphical user interface (GUI): users can see files, folders, etc. graphically (on the left of your binder)
- Command-line interdaces (CLI): users interact with computer via command line (Terminal on the right of your binder)
If we are using GUI with too many clicks, we can use CLI to help us.
Unix concept 1: Navigating files
To find out where we are, we can use pwd to print out current working directory.
/cloud/project$ pwd
/cloud/project
Check files in the current directory (current folder) using ls command (listing). You should have four items in your current directory as shown below.
/cloud/project$ ls
data-shell unix_intro
If you want to annotate folders when using ls command, we can use a flag ls -F is listing with flag-F to indicate directory/folder.
/cloud/project$ ls -F
data-shell/ unix_intro/
Practice question 1: What does the command ls do when using with -l and -h flags?
Check files in other directory using ls Directory_name, you will see that there are four items in unix_intro folder.
/cloud/project$ ls unix_intro/
data example.txt experiment six_commands
Now, we know which directory we want to work with, let’s change working directory using cd command.
/cloud/project$ cd unix_intro/
/cloud/project/unix_intro$
Now we know how to go down directory, how do we go up/back?
/cloud/project/unix_intro$ cd project
bash: cd: project: No such file or directory
To take us back to parent directory, we do cd .., let’s try
/cloud/project/unix_intro$ cd ..
/cloud/project$
We can also use a path to change directory.
/cloud/project$ cd unix_intro/experiment/
/cloud/project/unix_intro/experiment$
Change to home directory in one command, cd
/cloud/project/unix_intro/experiment$ cd
/cloud/project$
Unix concept 2: Working with files
We know how to navigate files, how can we create, copy, or delete files?
Let’s make sure we start at unix_intro folder and take a look at what we have in this folder using ls -F.
/cloud/project$ cd unix_intro/
/cloud/project/unix_intro$ pwd
/cloud/project/unix_intro
/cloud/project/unix_intro$ ls -F
data/ example.txt experiment/ six_commands/
Currently, there are three directories/folders, to create a new directory, we will use mkdir command.
/cloud/project/unix_intro$ mkdir Thesis
Check if you have Thesis directory, there should be five items in your unix_intro directory.
/cloud/project/unix_intro$ ls -F
data/ example.txt experiment/ six_commands/ Thesis/
Note for naming files and directiries: 1) don’t use whitespaces, 2) don’t begin with - (dash), 3) stick with letters, numbers, . (period or full stop), - (dash), and _ (underscore). Referent to swcarpentry
Now, change working directory to Thesis and we will create a file called draft.txt using vim command.
/cloud/project/unix_intro$ cd Thesis/
/cloud/project/unix_intro/Thesis$ vim draft.txt
Once you open up vim it will look like a picture below. Let’s write a sentence into your file. Press i to activate insert mode, then press esc to exit after you’re done writing. To save file, type :w and press enter. To exit from vim, type :q and press enter.
Check for draft.txt in your Thesis directory
/cloud/project/unix_intro/Thesis$ ls -lh
total 4.0K
-rw-rw---- 1 r1200493 rstudio-user 19 Aug 23 10:39 draft.txt
Create a file without nano using touch command, let’s try
/cloud/project/unix_intro/Thesis$ touch my_file.txt
Practice question 2: What did the touch command do? When you look at your home directory using the GUI file explorer, does the file show up?
Preactice question 3: Try using ls -l to inpsec the files, do you see any different between draft.txt and my_file.txt?
We know how to create a file, how do we delete/remove file?
We cab use rm command, however, there is no trash bin. Removing/deleting is FOREVER!!! Be Careful!!!
/cloud/project/unix_intro/Thesis$ rm draft.txt
What about removing directory? Let’s move up/back to unix_intro and try removing Thesis directory
/cloud/project/unix_intro/Thesis$ cd ..
/cloud/project/unix_intro$ rm Thesis
rm: cannot remove 'Thesis': Is a directory
You will get an error. To remove directory, we can use rm -r Thesis and your Thesis will be removed.
/cloud/project/unix_intro$ rm -r Thesis/
How do we change file name? We can use mv command.
#lisitng files and folder
/cloud/project/unix_intro$ ls
data example.txt experiment six_commands
#change file name using mv command
/cloud/project/unix_intro$ mv example.txt example_1.txt
#listing files and folder, you should see that example.txt becomes example_1.txt
/cloud/project/unix_intro$ ls
data example_1.txt experiment six_commands
We can also use mv command to move file.
# move a file
/cloud/project/unix_intro$ mv example_1.txt data/
# now a file has been moved to data folder
/cloud/project/unix_intro$ ls data/
all_samples example_1.txt
How about copy file instead if moving file?
#copy file to current directory
/cloud/project/unix_intro$ cp data/example_1.txt .
#listing files and folders, example_1.txt should be present in your current working directory
/cloud/project/unix_intro$ ls
data example_1.txt experiment six_commands
Practice question 4: Suppose that you created a .txt file in your current directory to contain a list of the statistical tests you will need to analyze your data, and named it: statstics.txt
After creating and saving this file you realize you misspelled the filename! You want to correct the mistake, which of the following commands could you use to do so? Please explain why?
cp statstics.txt statistics.txtmv statstics.txt statistics.txtmv statstics.txt .cp statstics.txt .
Lastly, there are many useful commands that were not covered in this tutorial, but I hope that this tutorial and system will make you feel more comfortable using CLI.
References