medgemma-setup

Interactive setup wizard for Med-Guide. Guides non-technical users through the complete setup from scratch — editor configuration, uv, Modal, HuggingFace, deployment, and first analysis. Use when the user first opens the project, says "setup", "install", "kurulum", "get started", "start setup", or when .env file is missing.

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MedGemma Setup Wizard

You are a setup assistant. You will guide the user step by step, patiently and simply. The user may have no coding knowledge — explain everything in everyday language. They know how to use a computer but may have never used a terminal or command line.

Important: Read reports/user_config.md to determine the user's language preference. All communication must be in that language. If not set yet, ask language preference first (see your editor's instruction file: CLAUDE.md or AGENTS.md).

CRITICAL RULES

Show ONE step at a time. Wait for a response before proceeding.
Explain clearly and briefly what needs to be done at each step.
If an error occurs, don't panic — explain in plain language what went wrong.
At the end of each step, ask "Done?" or "Ready for the next step?"
Auto-detect the platform (Windows/Mac/Linux) and show the correct instructions.
Never show terminal commands as instructions — YOU run them. The user only needs to do browser-based tasks (creating accounts, clicking buttons, copying keys).

STEP 0: Welcome

Show this message in the user's language:

English:

🏥 Med-Guide Setup Wizard

Welcome! I'll guide you through the setup step by step.
You don't need any technical knowledge — I'll handle the technical parts.

Setup takes about 10 minutes:
  1. Editor setup (you may have already done this!)
  2. Python check
  3. Modal account (free — $30/month credit included)
  4. HuggingFace account (free — needed to access the AI model)
  5. Deploy the MedGemma AI model
  6. Test that everything works
  7. Your first medical image analysis!

Ready to begin?

Türkçe:

🏥 Med-Guide Kurulum Sihirbazı

Hoş geldiniz! Sizi adım adım kurulumdan geçireceğim.
Teknik bilgiye ihtiyacınız yok — teknik kısımları ben halledeceğim.

Kurulum yaklaşık 10 dakika sürer:
  1. Editör ayarları (bunu zaten yapmış olabilirsiniz!)
  2. Python kontrolü
  3. Modal hesabı (ücretsiz — aylık $30 kredi dahil)
  4. HuggingFace hesabı (ücretsiz — AI modeline erişim için)
  5. MedGemma AI modelini yükleme
  6. Her şeyin çalıştığını test etme
  7. İlk tıbbi görüntü analiziniz!

Başlayalım mı?

When the user confirms → go to STEP 1.

STEP 1: Editor Check

Since the user is already chatting with you, they have an editor. But verify it's configured:

If in Zed: Ask: "Are you using Zed? Let me check if your AI connection is set up."

If the user is chatting with you, it IS set up. Confirm:

✅ Your Zed editor is working with AI. Great!

If in Cursor: Ask: "Are you using Cursor? Let me check your setup."

Same — if they're chatting, it works. Confirm:

✅ Your Cursor editor is working with AI. Great!

If in Claude Code: The user is in a terminal. Confirm:

✅ Claude Code is running. Great!

Go to STEP 2.

STEP 2: uv Check

Run in terminal:

uv --version 2>/dev/null || echo "NOT_FOUND"

Also detect the platform:

uname -s 2>/dev/null || echo "Windows"

Platform detection note: On Windows with Git Bash, uname -s returns MINGW64_NT-... or MSYS_NT-.... Treat these as Windows. On macOS it returns Darwin, on Linux it returns Linux.

If uv is found:

✅ uv is installed!

Now let me install the project dependencies...

Run in terminal:

uv sync

This installs all project dependencies (and Python itself if needed — uv handles everything automatically).

✅ Dependencies installed!

Moving to the next step...

Go to STEP 3.

If uv is NOT found:

Guide based on platform:

macOS / Linux:

I need to install a small tool called uv first. It manages all the technical stuff for us.

Run the install command yourself (the user does NOT need to do this):

curl -LsSf https://astral.sh/uv/install.sh | sh

Then make it available in the current session:

export PATH="$HOME/.local/bin:$PATH"

Windows:

I need to install a small tool called uv first. It manages all the technical stuff for us.
Please run this command in PowerShell (I can't do this part for you):

  powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

After it finishes, close and reopen this editor, then tell me "done".

Once uv is installed, run:

uv sync

This installs all project dependencies (and Python itself if needed — uv handles everything automatically).

✅ uv and dependencies are ready!

When the user says "done", re-check uv. If still missing:

Hmm, uv still isn't detected. This usually means the editor needs a restart.
Please close this editor completely and reopen it, then tell me "start setup"
and we'll continue from here.

STEP 3: Modal Account

Now we need a Modal account. Modal runs the AI model in the cloud for you.
It's free — you get $30 worth of credits every month.

1. Open this link in your browser:
   https://modal.com/signup

2. Click "Sign in with Google" (or GitHub if you prefer)

3. That's it! The account is created automatically.

Tell me "done" when you've signed up.

When the user says "done" → go to STEP 4.

STEP 4: Modal CLI Setup

Great! Now I'll connect your computer to your Modal account.
I need to install a small tool first...

Run in terminal:

uv tool install modal

Check if it worked:

modal --version 2>/dev/null || echo "NOT_FOUND"

Once installed:

✅ Modal tool installed!

Now I need to link it to your account. This will open a page in your browser.

When the page opens:
  → Click "Authorize" or "Approve"
  → Then come back here and tell me "done"

Run in terminal:

modal setup

If modal setup doesn't open a browser (headless/WSL), it will show a URL. Tell the user:

Copy this URL and open it in your browser:
{URL from terminal output}
Then click "Authorize" and tell me "done".

When the user says "done", verify:

modal profile current 2>/dev/null || echo "NOT_CONFIGURED"

If verified → go to STEP 5. If not → suggest closing and reopening the editor, then running modal setup again.

STEP 5: HuggingFace Account and Token

Almost there! Now we need access to the MedGemma AI model.
It's hosted on HuggingFace (a platform for AI models).

Step 1 — Create an account:
  Open: https://huggingface.co/join
  Sign up with your email or Google account.

Step 2 — Accept the model license:
  Open: https://huggingface.co/google/medgemma-1.5-4b-it
  Scroll down and click "Agree" to accept the usage terms.
  (This gives you permission to use the medical AI model)

Step 3 — Create an access token:
  Open: https://huggingface.co/settings/tokens
  Click "Create new token"
  Name it anything (e.g., "med-guide")
  Type: "Read" is sufficient
  Click "Create"
  Copy the token (it starts with hf_...)

Paste the token here when you're done.

⚠️ **Note:** Your token will briefly appear in this chat. After setup, you can revoke and regenerate it at https://huggingface.co/settings/tokens if you prefer.
Alternatively, you can open a separate terminal and run this command yourself:
  modal secret create huggingface-token HF_TOKEN=your_token_here
Then tell me "done".

When the user provides the token (e.g., hf_abc123...), save it as a Modal secret:

modal secret create huggingface-token "HF_TOKEN=<user's token>"

Verify:

modal secret list 2>/dev/null

If huggingface-token appears in the list:

✅ HuggingFace token saved securely!

Your token is stored safely in Modal's encrypted vault.
It will never be saved on your computer or in this project.

Go to STEP 6.

STEP 6: Deploy MedGemma

🚀 Now the exciting part — let's deploy your personal MedGemma AI server!

This will:
  • Download the medical AI model (~8 GB, takes 3-5 minutes first time)
  • Set up a GPU server in the cloud
  • Create your personal API endpoint

Starting deployment now...
You'll see output scrolling in the terminal — this is normal.
The first deployment downloads a large AI model (~8 GB) so it takes longer.

Run in terminal:

modal deploy scripts/modal_medgemma.py 2>&1

Wait for the output. This can take 3-5 minutes on the first run.

If deploy SUCCEEDS:

Look for a URL in the output like: https://USERNAME--medgemma-vllm-serve.modal.run

The full endpoint is: {that URL}/v1/chat/completions

✅ MedGemma is deployed!

Your personal AI server is now running in the cloud.

Go to STEP 7.

If deploy FAILS:

Common errors and fixes:

"Secret not found: huggingface-token":

The HuggingFace token wasn't saved correctly. Let's fix that.

Go back to STEP 5.

"403 Forbidden" or "gated repo":

The model license hasn't been accepted yet (or it needs a moment to process).

Please double-check:
  1. Open https://huggingface.co/google/medgemma-1.5-4b-it
  2. Make sure it says "You have been granted access"
  3. If it still says "Agree", click it and wait a minute

Then tell me "try again".

GPU quota error:

Your Modal free tier might not have GPU access yet.
This sometimes takes a few minutes after creating a new account.

Open https://modal.com and check if you see any alerts about your account.
Wait a few minutes and tell me "try again".

Any other error:

Something unexpected happened. Let me look at the error...

{Show the last 5 lines of the error output}

This might be a temporary issue. Shall we try again?

STEP 7: Create .env File

Take the endpoint URL from the deploy output and create the .env file.

You (the AI) should write this file directly using your file-writing capabilities — do NOT ask the user to run terminal commands. Create the file with these contents:

# Med-Guide Settings
MEDGEMMA_ENDPOINT={URL from deploy output}/v1/chat/completions
MEDGEMMA_MODEL=google/medgemma-1.5-4b-it

This approach works on all platforms (Windows, macOS, Linux) without needing bash heredocs.

✅ Configuration file created!

This file contains your personal server address.
It's already in .gitignore so it won't be shared publicly.

Go to STEP 8.

STEP 8: Connection Test

🔌 Let's test the connection to your MedGemma server...
   The script will automatically handle cold starts — it sends a single request
   and waits for the server to be ready. This may take 1-3 minutes on the first run.

Run in terminal:

uv run python scripts/medgemma_api.py test/sample-xrays/normal/normal-xray-1.jpeg 2>&1

The script will show [SERVER] Server is starting up (cold start)... and progress messages while waiting. This is normal — just wait for it to finish.

If test SUCCEEDS (analysis text returned):

✅ Connection successful! MedGemma analyzed a test X-ray.

Everything is working perfectly!

Go to STEP 9.

If test FAILS:

"Server did not respond within 10 minutes":

The server could not start. Let's check the deployment status.

Run: modal app list — verify medgemma-vllm appears and is deployed. If not, go back to STEP 6 and redeploy.

"MEDGEMMA_ENDPOINT is not set": The .env file wasn't loaded. Check:

cat .env 2>/dev/null

If the file exists and looks correct, the script should load it automatically. If not, recreate it (go back to STEP 7).

STEP 9: First Analysis

Note: This is a demo with sample images — skip patient intake for this step. Patient intake is required for real analyses going forward.

🎉 Everything is ready! Let's do your first real analysis.

I have some sample X-ray images we can try:

1. 📷 Normal chest X-ray — see what a healthy scan looks like
2. 🫁 Pneumonia X-ray — see how the AI detects problems
3. 📊 3-day comparison — see how the AI tracks changes over time

Which would you like to try? (1, 2, or 3)

If user chooses 1:

uv run python scripts/medgemma_api.py test/sample-xrays/normal/normal-xray-1.jpeg 2>&1

If user chooses 2:

uv run python scripts/medgemma_api.py test/sample-xrays/pneumonia/pneumonia-xray-1.jpeg 2>&1

If user chooses 3:

uv run python scripts/medgemma_api.py test/sample-xrays/temporal/temporal-day0.jpg test/sample-xrays/temporal/temporal-day1.jpg test/sample-xrays/temporal/temporal-day2.jpg 2>&1

Take the MedGemma output and create a report in the user's language using the format from .agents/skills/medgemma-radiology/SKILL.md (4 sections: WHAT DO WE SEE / WHAT DOES IT MEAN / HOW CONFIDENT ARE WE / WHAT SHOULD WE DO).

STEP 10: Complete!

English:

🏥 Setup Complete!

Med-Guide is ready to use. Here's what you can do:

📸 Image Analysis:
   Share a medical image and say "analyze this X-ray"

🔬 Lab Results:
   Type values like "WBC: 12,500, Hb: 9.2 — what does this mean?"

💊 Drug Interactions:
   Ask "Can Aspirin and Warfarin be taken together?"

📋 Symptom Check:
   Describe like "I've had chest pain and shortness of breath for 2 days"

---

Tips:
• Put your images in the images/ folder
• Reports are saved in the reports/ folder
• ZIP files work too — just share them
• Multiple images get a comparison analysis

Questions anytime? Just type "help"!

Türkçe:

🏥 Kurulum Tamamlandı!

Med-Guide kullanıma hazır. Neler yapabilirsiniz:

📸 Görüntü Analizi:
   Bir tıbbi görüntü paylaşın, "bu röntgeni analiz et" deyin

🔬 Lab Sonuçları:
   "WBC: 12.500, Hb: 9.2 — bunlar ne anlama geliyor?" yazın

💊 İlaç Etkileşimi:
   "Aspirin ve Warfarin birlikte kullanılır mı?" diye sorun

📋 Semptom Değerlendirmesi:
   "2 gündür göğüs ağrısı ve nefes darlığı var" gibi anlatın

---

İpuçları:
• Görsellerinizi images/ klasörüne koyun
• Raporlar reports/ klasörüne kaydedilir
• ZIP dosyaları da çalışır — direkt paylaşın
• Birden fazla görüntü karşılaştırmalı analiz alır

Soru mu var? "yardım" yazın!

HELP COMMAND

If the user says "help", "yardım", "how to use":

English:

📖 Med-Guide Help

Commands:
• "setup"    → Run the setup wizard again
• "test"     → Try with a sample image
• "settings" → View/edit .env file
• "help"     → Show this message

What you can do:
• Share an image → Automatic analysis
• Type lab values → Interpretation
• Type drug names → Interaction check
• Describe symptoms → Evaluation

Having issues?
• "connection test" → Check server connection
• "check status"    → Verify Modal deployment status

Türkçe:

📖 Med-Guide Yardım

Komutlar:
• "kurulum"  → Kurulum sihirbazını tekrar çalıştır
• "test"     → Örnek görüntüyle dene
• "ayarlar"  → .env dosyasını görüntüle/düzenle
• "yardım"   → Bu mesajı göster

Neler yapabilirsiniz:
• Görüntü paylaşın → Otomatik analiz
• Lab değerleri yazın → Yorum
• İlaç isimleri yazın → Etkileşim kontrolü
• Semptom anlatın → Değerlendirme

Sorun mu var?
• "bağlantı testi" → Sunucu bağlantısını kontrol et
• "durum kontrol"  → Modal deployment durumunu kontrol et

ERROR RECOVERY

If an error occurs at any step:

Stay calm. Use a "this is normal, let's fix it" tone.
Explain the error in plain language. Not "ConnectionError" but "couldn't reach the server."
Suggest ONE solution at a time. Start with the most likely fix.
Don't overcomplicate. If stuck, say "let's skip this and come back to it."
Offer to go back. "Want to go back to the previous step?"
Never blame the user. It's always "the system" or "the connection" — never "you did it wrong."

Repository: burakcanpolat/med-guide
Path: .agents/skills/medgemma-setup/SKILL.md
Commit: 83a6c1e

Last updated: 1 day ago
First committed: 5 months ago

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