Tutorial

Loops and Variables

45 Minutes

Objectives

• Read and write a for loop that runs a command on each file.
• Use variables, braces and quotes so values expand the way you expect.
• Make a script stop on errors and on unset variables.

Prerequisite

• You can write and submit a batch script. See Submitting Your First Job.
• Following on from Measuring Job Efficiency is useful, but not needed.

Skipped ahead? Set up here

Loops over files

Command substitution

Variables for file paths

Rewrite the loop

Solution

Braces and quotes

#

Braces

What does this print?

number=01
echo $numbersample.txt

.txt

Bash reads $numbersample, a variable that is not set, so it expands to nothing.

01sample.txt

That needs braces: ${number}sample.txt.

An error saying numbersample is not set.

Only with set -u. Without it, bash carries on silently.

Stopping on errors

#

Unset variables

A script starts with set -u and then runs mkdir "${resluts}/vcf", misspelling results. What happens?

The script stops with an error that resluts is unbound.

It creates a directory called /vcf.

That is what happens without set -u, as the variable expands to nothing.

It creates results/vcf.

Keypoints

• A for loop runs the same commands on each file.
• Variables make a script easier to read and to change in one place.
• Use braces and quotes so variables expand the way you expect.
• #!/bin/bash -e and set -u stop a script at the first error or unset variable.

What next

• Next lesson: Reusable Job Scripts.
• For more shell practice: the Software Carpentry Unix Shell lessons on loops and shell scripts.

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