Scripts¶

Learning objectives

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

For teachers

Teaching goals are:

.

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?

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?

Here is a video that shows the solution of these exercises

Exercise 1: write a bash script¶

Create a file called do_cowsay.sh with the content below:

module load cowsay/3.03
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!

Try to find how to run the script (without making the file executable)

Answer

To run the script, use:

bash my_script.sh

Try to find how to make the script executable

Answer

To make the script executable, do:

chmod +x my_script.sh

Run the script without calling bash

Answer

To run the script:

./my_script.sh

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@rackham1 ~]$ ./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