Shell Scripting Basics

Automate repetitive tasks by combining commands into scripts.

Step 1: Create Your First Script

# Create a simple script
cat > hello.sh << 'EOF'
#!/bin/bash
echo "Hello, World!"
echo "Today is $(date +%Y-%m-%d)"
EOF

# View it
cat hello.sh

#!/bin/bash
echo "Hello, World!"
echo "Today is $(date +%Y-%m-%d)"

# Make it executable and run
chmod +x hello.sh
./hello.sh

Hello, World!
Today is 2026-01-20

Step 2: Using Variables

cat > variables.sh << 'EOF'
#!/bin/bash
# Variables (no spaces around =)
NAME="Student"
COUNT=5

echo "Hello, $NAME"
echo "Count is $COUNT"

# Command substitution
TODAY=$(date +%Y-%m-%d)
NUM_FILES=$(ls | wc -l)
echo "Today: $TODAY, Files in directory: $NUM_FILES"
EOF

chmod +x variables.sh
./variables.sh

Hello, Student
Count is 5
Today: 2026-01-20, Files in directory: 12

Step 3: Command Line Arguments

cat > args.sh << 'EOF'
#!/bin/bash
echo "Script: $0"
echo "First arg: $1"
echo "Second arg: $2"
echo "All args: $@"
echo "Num args: $#"
EOF

chmod +x args.sh
./args.sh apple banana cherry

Script: ./args.sh
First arg: apple
Second arg: banana
All args: apple banana cherry
Num args: 3

Step 4: If Statements

cat > checker.sh << 'EOF'
#!/bin/bash
if [ -z "$1" ]; then
    echo "Usage: $0 <filename>"
    exit 1
fi

if [ -f "$1" ]; then
    echo "$1 is a file"
elif [ -d "$1" ]; then
    echo "$1 is a directory"
else
    echo "$1 does not exist"
fi
EOF

chmod +x checker.sh
./checker.sh genes.txt

genes.txt is a file

./checker.sh find_test

find_test is a directory

Test operators: -f (file exists), -d (directory), -z (empty string), -eq (equal), -gt (greater than)

Step 5: For Loops

cat > loop.sh << 'EOF'
#!/bin/bash
# Loop over files
for file in *.txt; do
    echo "Found: $file"
done

# Loop with range
for i in {1..3}; do
    echo "Count: $i"
done
EOF

chmod +x loop.sh
./loop.sh

Found: genes.txt
Found: sample.txt
Found: testfile.txt
Count: 1
Count: 2
Count: 3

Challenge: Bioinformatics Script

Create a script that counts lines in all .txt files:

cat > count_lines.sh << 'EOF'
#!/bin/bash
for file in *.txt; do
    lines=$(wc -l < "$file")
    echo "$file: $lines lines"
done
EOF

chmod +x count_lines.sh
./count_lines.sh

genes.txt: 5 lines
sample.txt: 5 lines
testfile.txt: 1 lines

BCH709 Introduction to Bioinformatics: Shell Scripting Basics