Skip to content

Scripts

Learning outcomes

  • Practice using the UPPMAX documentation
  • Can create a script
  • Can make a script executable
  • Can run a script
For teachers

Teaching goals are:

  • Learners have created a script
  • Learners have made a script executable
  • Learners have run a script

Lesson plan:

gantt
  title Scripts
  dateFormat X
  axisFormat %s
  section First hour
  Prior : prior, 0, 5s
  Present: present, after prior, 2s
  %% It took me 8 mins, here I do that time x2
  Challenge: crit, challenge, after present, 16s
  %% Here I use the same time it took me to give feedback
  Feedback: feedback, after challenge, 8s

Prior questions:

  • What is a script?
  • Why would you want to use a script?
  • How to write a script?

Feedback questions:

  • Why would you want to use a script?
  • What should you not forget when writing a script?
  • Which group of programming languages can you directly call from a script? Could you give an example?

Why?

Scripts allow you to run multiple commands after each other, such as loading modules and then running your favorite software.

Exercises

Need a video?

See this YouTube video that shows the solution of these exercises

Pelle works the same a Rackham in these contexts.

Exercise 1: write a bash script

  • Create a file called do_cowsay.sh with the content below:
module load cowsay/3.04
cowsay hello
Answer

This is just creating a file, which can be done in many ways, such as using touch and nano. In whatever way you did it, it's good enough!

Answer

To run the script, use:

bash my_script.sh
Answer

To make the script executable, do:

chmod +x my_script.sh

or:

chmod u+x my_script.sh
  • Run your (executable) script directly (i.e. without calling bash)
Answer

To run the script:

./my_script.sh
  • (optional) Why does the script has a .sh file extension? Search the web for an answer.
Answer

This is a social convention: it allows a human to see that a file is a so-called shell script. It is no coincidence that .sh are the last two letters of bash.

Exercise X1: write an executable script in your favorite programming language

  • Create a script in your favorite programming language, with the following name and content:
Programming language Script name
Python my_script.py
R my_script.R
Programming language Script content
Python print("Hello from Python")
R message("Hello from R")
Answer

This is just creating a file, which can be done in many ways, such as using touch and nano. In whatever way you did it, it's good enough!

  • Make the script executable
Answer

To make the script executable, do:

Programming language Command
Python chmod +x my_script.py
R chmod +x my_script.R
  • Run the script. What is the error message?
Answer

How to run the script:

Programming language How to run the script
Python ./my_script.py
R ./my_script.R

Error message:

[sven@pelle1 ~]$ ./my_script.py 
./my_script.py: line 1: syntax error near unexpected token `"Hello from Python"'
./my_script.py: line 1: `print("Hello from Python")'

[sven@pelle1 ~]$ ./my_script.R
./my_script.R: line 2: syntax error near unexpected token `"Hello from R"'
./my_script.R: line 2: `message("Hello from R")'
  • At the start of your R script, add a first line, as shown in the table below. This is called the 'shebang'. The shebang tells bash with which program to run the script when it is executable
Programming language First line to add
Python #!/bin/env python
R #!/bin/env Rscript
  • Run the script again and confirm that it works