BCH709 Introduction to Bioinformatics: Environment Variables

Environment Variables

Environment variables store system settings and user preferences that programs can access.

Step 1: View Your Environment

# See common variables
echo "Home directory: $HOME"
echo "Current user: $USER"
echo "Current shell: $SHELL"
echo "Current directory: $PWD"

Home directory: /home/username
Current user: username
Current shell: /bin/bash
Current directory: /home/username/permission_practice

# View PATH (where system looks for commands)
echo $PATH

/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin

Common Environment Variables

Step 2: Create and Use Variables

# Create a variable (no spaces around =)
MYNAME="Student"
echo "Hello, $MYNAME"

Hello, Student

# Export makes it available to child processes
export PROJECT_DIR="$HOME/myproject"
echo $PROJECT_DIR

/home/username/myproject

# Unset removes a variable
unset MYNAME
echo "Name is: $MYNAME"

Name is:

Step 3: Make Variables Permanent

Add to ~/.bashrc for permanent variables:

# View current bashrc (last 5 lines)
tail -5 ~/.bashrc

# Add a custom variable (be careful with >>)
echo 'export BIOINF_DATA="$HOME/biodata"' >> ~/.bashrc

# Reload bashrc
source ~/.bashrc

# Verify
echo $BIOINF_DATA

/home/username/biodata