Issue Summary

The ./init.sh script, which initializes the cBioPortal Docker setup, lacks strict error handling. When a sub-script or command fails, the script continues execution silently, making it difficult for users to diagnose issues—especially on non-Linux systems. Improving error handling will enhance reliability and provide better feedback to contributors.

Problem Description

• The script orchestrates multiple sub-scripts responsible for setting up dependencies, environment variables, and databases.
• If a sub-script fails, the failure is not always surfaced due to missing error checks, causing the setup to appear successful while being incomplete.
• This issue is more prominent on Windows/macOS, where certain shell commands behave differently, leading to hidden failures.
• Logs do not always provide clear error messages, making debugging difficult.

Proposed Solution

To improve the robustness of the ./init.sh script, I propose the following changes:

1. Fail Fast on Errors

   • Enforce strict error handling using set -e to terminate the script when any command fails.
   • Use trap to capture errors and print meaningful messages before exiting.

2. Improve Logging and Debugging

   • Implement set -x as an optional debug mode to display executed commands.
   • Add clearer error messages to guide users when failures occur.

3. Cross-Platform Compatibility Enhancements

   • Identify problematic shell commands that may behave inconsistently across different platforms.
   • Replace or document environment-specific dependencies for better cross-OS support.

4. Enhance Documentation

   • Update the documentation to include common troubleshooting steps and error-handling mechanisms.

Steps to Reproduce the Issue

1. Clone the cbioportal-docker-compose repository and follow the setup instructions.
2. Run ./init.sh on a non-Linux system (e.g., Windows WSL or macOS).
3. Observe that certain failures occur silently, leading to an incomplete setup.

Expected Behavior

• The script should halt immediately when an error occurs.
• The failure reason should be clearly logged.
• Contributors should be able to diagnose and fix issues more efficiently.

Additional Context

• This issue is particularly relevant for new contributors who may struggle with silent failures.
• Improving error handling will make onboarding smoother and debugging easier.
• Happy to work on this and submit a PR!