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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.

(Optional) Exercise 2: write an executable R script

  • Create a file called my_r_script.R with the content below:
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:

chmod +x my_r_script.R
  • Run the script. What is the error message?
Answer

This is how to run the script and the error message:

[sven@pelle1 ~]$ ./my_r_script.R
./my_r_script.R: line 2: syntax error near unexpected token `"Hello from R"'
./my_r_script.R: line 2: `message("Hello from R")'

  • At the start of your R script, add #!/bin/env Rscript. This is called the 'shebang'. The shebang tells bash with which program to run the script when it is executable

  • Run the script again and confirm that it works