Troubleshooting & Resources

Common problems and where to get help

Docker Issues

Having trouble with Docker Desktop? Here are solutions to the most common problems.

Docker Desktop won't start (Windows)

  • WSL 2 not installed: Open PowerShell as Administrator and run wsl --install, then restart your computer
  • Virtualization disabled: Enable virtualization in your BIOS/UEFI settings. Restart your computer and enter BIOS (usually F2, F10, or Delete key during startup), then look for "Intel VT-x" or "AMD-V" and enable it
  • Windows version too old: Update Windows to at least Build 19041 or higher. Check your version by pressing Win + R, typing winver, and pressing Enter
  • Hyper-V conflicts: Ensure "Use WSL 2 instead of Hyper-V" is selected during Docker installation. If you need Hyper-V, you may need to use Docker with Hyper-V backend instead

Docker Desktop won't start (Mac)

  • Permission issues: Check System Preferences → Security & Privacy for permission requests. Docker needs permissions to install system extensions
  • Apple Silicon (M1/M2/M3): Ensure Rosetta 2 is installed. Run in Terminal: softwareupdate --install-rosetta
  • macOS version: Verify macOS version is 11 (Big Sur) or newer. Older versions are not supported
  • File sharing: Go to Docker Desktop → Preferences → Resources → File Sharing and ensure your home directory is listed
  • Docker daemon not responding: Quit Docker completely (right-click Docker icon → Quit Docker Desktop) and restart it

"docker: command not found"

  • Docker Desktop not running: Ensure Docker Desktop is running (check system tray for Docker icon on Windows, menu bar on Mac)
  • PATH not updated: Close and reopen PowerShell/Terminal after Docker installation. The installation adds Docker to your system PATH
  • Installation incomplete: Restart your computer if the problem persists after reopening terminal
  • Windows specific: Try running docker.exe --version instead. If this works, there's a PATH configuration issue

Container won't pull

  • Network issues: Check your internet connection. Docker Hub requires a stable connection to download large images
  • Docker not running: Verify Docker Desktop is running and shows "Running" status
  • Specify tag explicitly: Try pulling with specific tag: docker pull cosmelab/entm201l:latest
  • Firewall/proxy: If you're on a university network, firewall or proxy settings may block Docker Hub. Contact IT or try from home network
  • Disk space: Ensure you have enough disk space (at least 5-10 GB free). Docker images can be large
  • Rate limits: Docker Hub has pull rate limits. If you've pulled many images recently, wait an hour or create a free Docker Hub account and login: docker login

Container exits immediately after starting

  • Missing -it flags: Ensure you're running with docker run -it (interactive terminal) for containers that need user input
  • Port conflicts: If using -p 8888:8888, make sure port 8888 isn't already in use by another program
  • Check logs: Run docker logs <container-name> to see error messages
  • Volume mount issues: Verify the path you're mounting exists. On Windows, use forward slashes or escape backslashes

GitHub Issues

Problems with GitHub account setup, Student Pack, or Copilot? Solutions here.

Student Pack not approved

  • Approval time: GitHub Student Developer Pack approval typically takes 1-3 days. Sometimes it can take up to a week during busy periods (start of semester)
  • Check verification method: If you uploaded a document, make sure it clearly shows your name, current enrollment status, and expected graduation date
  • UCR email verification: Ensure you used your @ucr.edu email address and verified it (check spam folder for verification email)
  • Reapply if rejected: If your application was rejected, carefully read the rejection reason and reapply with better documentation (enrollment verification from UCR Student Portal)
  • Contact GitHub Education: If it's been more than 2 weeks, contact GitHub Education support at support.github.com/contact/education

Copilot not working

  • Student Pack required: GitHub Copilot requires approved Student Developer Pack. Check education.github.com/pack to verify your status
  • VS Code not signed in: Ensure you're signed into GitHub in VS Code. Click the account icon in the bottom left, then "Sign in to Sync Settings"
  • Extension not installed: Open Extensions (Ctrl+Shift+X / Cmd+Shift+X), search for "GitHub Copilot", and install if missing
  • Copilot disabled: Check the bottom status bar in VS Code for Copilot icon. If it says "Disabled" or has a red X, click it and enable Copilot
  • File type not supported: Copilot works best with popular languages (Python, JavaScript, etc.). It may not work in plain text files
  • Restart VS Code: After installing Copilot extension, completely quit and restart VS Code
  • Check subscription: Go to github.com/settings/copilot to verify your Copilot subscription is active

Repository access problems

  • 404 error: Make sure you've accepted the assignment invitation first. You won't see the repository until you click the assignment link
  • Permission denied (git push): Ensure you're authenticated. Run git config --global user.name "Your Name" and git config --global user.email "your@ucr.edu"
  • HTTPS vs SSH: If you're getting authentication errors, try cloning with HTTPS instead of SSH, or vice versa
  • Personal access token: GitHub no longer accepts password authentication. Generate a personal access token at github.com/settings/tokens and use it instead of your password
  • Not in organization: Make sure your instructor has added you to the course organization. Check your email for GitHub organization invitations

Git command issues

  • Merge conflicts: If you see "CONFLICT" messages, edit the conflicted files (look for <<<<<<< markers), remove the markers, save, then git add . and git commit
  • Detached HEAD: If you accidentally checked out a commit, run git checkout main to return to the main branch
  • Undo last commit: If you committed by mistake, run git reset --soft HEAD~1 to undo (keeps your changes)
  • Files not updating: After pulling, if files don't update, check if you have uncommitted changes blocking the pull. Commit or stash them first

Resources

Official documentation and learning resources for the tools we use in this course.

Docker Resources

GitHub Student Benefits

Bioinformatics Tools Documentation

Get Help

Still stuck? Here's how to get help from your instructor and classmates.

Contact Instructor

Your instructor is here to help! Reach out via:

  • Email: Check Canvas or the course syllabus for instructor email
  • Office Hours: Attend weekly office hours (schedule on Canvas)
  • Canvas Messages: Send a message through Canvas inbox

Tips for getting help faster:

  • Include error messages (screenshots or copy-paste)
  • Describe what you were trying to do when the error occurred
  • Mention your operating system (Windows, Mac, Linux)
  • List what you've already tried

GitHub Issues on Course Repo

Found a bug in course materials or container? Report it!

  • Click "New Issue" to report problems with Docker container errors, broken links, missing dependencies, or unclear documentation
  • Check existing issues first - your problem may already be reported and solved!

Remember: There are no "stupid questions" in this class! Software setup can be tricky, and we're here to help everyone succeed. Don't hesitate to reach out!