Bash Scripting: Automating Your Bioinformatics Workflows

In Part 1, we learned how to navigate the Linux terminal. But imagine this: You have 50 FASTQ files from a sequencing run. Are you going to type a command 50 times?

No. In bioinformatics, if you have to do something more than twice, you should script it.

Today, we dive into Bash Scripting - the art of giving the computer a "To-Do List" that it can execute while you go grab a coffee.

1. What is a Bash Script?

A Bash script is simply a text file containing a series of commands. It always starts with a "Shebang" line: #!/bin/bash. This tells the computer, "Hey, use the Bash shell to read this!"

Creating your first script:

1. Type nano myscript.sh

2. Add the following:

   #!/bin/bash
   echo "Starting the BioInfoQuant Analysis Pipeline..."
   mkdir -p processed_data
   ls -lh
   echo"Step 1 Complete."

3. Save and exit (Ctrl+O, Enter, Ctrl+X).
4. Make it executable: chmod +x myscript.sh
5. Run it: ./myscript.sh

2. The Power of Variables

Variables allow you to store data for later use. In bioinformatics, we use them to store file paths or sample names.

SAMPLE="Sample_A1"
echo "Processing $SAMPLE now..."

3. The "For Loop": The Bioinformatician’s Superpower

This is the most important tool in your kit. A loop allows you to repeat a command for every file in a folder.

Practical Example: Compressing all FASTA files at once

for file in *.fasta
do
   echo "Compressing $file..."
   gzip $file
done

Practical Example: Automating GROMACS (Energy Minimization) If you have multiple protein-ligand complexes, you can automate the energy minimization step:

for dir in protein_complex_*
do
    cd $dir
    gmx grompp -f em.mdp -c coord.gro -p topol.top -o em.tpr
    gmx mdrun -v -deffnm em
    cd ..
done

4. Record Notes: Common Mistakes to Avoid

• Spaces Matter: In Bash, VAR = "data" (with spaces) will fail. It must be VAR="data".
• Permissions: If you get a "Permission Denied" error, remember to use chmod +x on your script.
• The Path: Always use pwd to ensure your script is looking in the right folder.

Practical Exercise for Students

Create a script named organize.sh that:

1. Creates three folders: scripts, data, and results.
2. Moves all .sh files into scripts.
3. Moves all .fastq or .fasta files into data.
4. Prints a message saying “Workspace Organized!”

Summary Checklist

• [ ] Use #!/bin/bash at the top.
• [ ] Use chmod +x to make the script "alive."
• [ ] Use Loops for repetitive file tasks.
• [ ] Use Comments (#) to explain what your code does.