Bash scripting

Google recommends using bash for all executable shell scripts:

Restricting all executable shell scripts to bash gives us a consistent shell language that's installed on all our machines. In particular, this means there is generally no need to strive for POSIX-compatibility or otherwise avoid "bashisms".

For practical examples and command-line usage, see the CLI guide.

Shebang

The shebang is the first line of a script and tells the system which interpreter to use to run the script. For bash scripts, use #!/bin/bash:

#!/bin/bash
# After the shebang, add comments to describe the script
echo "Hello, world!"

Executing scripts

To execute a script from the command line, make it executable:

chmod +x /path/to/script.sh

Then run it:

./path/to/script.sh

Try saving the "Hello, world!" script above to a file and running it after making it executable. (The .sh extension is optional.)

Resources

• man bash
• Bash Reference Manual
• Bash Guide
• Advanced Bash-Scripting Guide
• Safety First!
• Bashisms
• Bash Pitfalls
• Arrays in Bash
• Shell Script Templates
• Command Name Extensions Considered Harmful

For a quick reference, check out DevHints.io.

Special Variables and Commands

Special variables and commands can be very useful in bash scripts, particularly for interacting with command history:

Command	Description
!!	Repeat the last command.
!$	Last argument of the last command.
$_	Last argument of the last command.
!^	First argument of the last command.
$?	Exit status of the last command.
!n	Repeat command number n from history.
!!:n	The n-th argument of the last command.
!!:s/old/new/	Substitute old with new in the last command.
!cmd	Run the most recent command starting with cmd.
!+	Next command in the history list (after the current one).
!-n	The command n lines before the current command in history.
!!:p	Print the last command without executing it.
!!:x	Extract and display the x-th argument of the last command.

Examples

You ran a command without sudo and want to run it again with sudo:

$ apt update
E: Could not open lock file /var/lib/apt/lists/lock - open (13: Permission denied)
$ sudo !!

You performed a dry run with echo and want to run the command for real:

$ echo sudo apt-get install -y vim
$ !:2-*

Update and Upgrade Everything on Ubuntu

To update and upgrade all packages:

sudo apt-get update && sudo apt-get upgrade -y

Alternatively:

yes | sudo sh -c 'apt update && apt upgrade && apt dist-upgrade \
                 && apt autoremove && apt autoclean && apt clean'

Special text inside bash scripts

Multiline Comments

To add multiline comments in bash, use the following syntax:

: '
This is a
very neat comment
in bash
'

Here Documents

A here document allows you to pass multiple lines of input to a command without storing it in a file:

cat << EOF
This is a here document.
It can be used to pass multiple lines of input to a command.
EOF

More useful commands

Command	Description
ssh user@host 'bash -s' < script.sh	Run a local script on a remote machine.
md5sum ./*.fastq.gz > md5sums.txt	Generate a file with the MD5 checksums of all files in the current directory.
md5sum -c md5sums.txt	Check files against the MD5 checksums in a file.
du -ha --max-depth=1	Check the total size of each folder in the current directory.
free -h	Check current memory usage.

Loop across files of the same extension

Don't use ls or find. Instead, use a glob pattern:

for file in ./*.bam; do  # Loop across all .bam files in the current directory
    command "$file"      # Quote the variable to handle spaces in filenames
done

# single-line loop
for file in ./*.bam; do command "$file"; done

source

Safely change directories

Don't use cd without checking if it was successful. You might end up executing commands in the wrong directory.

cd /path/to/some/dir || exit  # Exit if the directory doesn't exist or is inaccessible
rm -rf *                      # This could be very bad if the cd failed

source

Correctly define functions

Don't use function to define functions! It's ugly and not portable. Just use the function name followed by parentheses. We'll know it's a function.

# bad
function myfunc {
    echo "Hello, world!"
}

# very bad
function myfunc() {
    echo "Hello, world!"
}

# good
myfunc() {
    echo "Hello, world!"
}

source

Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.
Page last updated on 2024-10-17.