Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@MCP Clinical Research Server Search ClinicalTrials.gov for phase 3 breast cancer trials"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
This project exposes an MCP server that can:
search ClinicalTrials.gov for studies by condition or keyword
fetch the latest stock price for a company ticker from Yahoo Finance
Create a virtual environment if you want one.
Install dependencies:
python -m pip install -e .
Set your PAT and the server endpoint:
export MCP_PAT="your_personal_access_token" export MCP_ACCESS_URL="http://localhost:8000/mcp" export MCP_HOST="0.0.0.0" export MCP_PORT="8000"
Start the server:
python -m mcp_clinical.server
or:
mcp-clinical
Related MCP server: Clinical Trials MCP Server
Your MCP client should connect to:
Auth header: Authorization: Bearer
The server expects the same token in the MCP_PAT environment variable when it starts.
server_access_info()
clinical_trials_search(condition, max_results=5)
get_company_price(ticker, range_name="1d")
condition: "breast cancer"
max_results: 5
ticker: "AAPL"
range_name: "1d"
The safest public setup is:
EC2 instance with a public IP or Elastic IP
security group allowing 22, 80, and 443 inbound
NGINX listening on 80/443 and proxying to the MCP app on 127.0.0.1:8000
systemd service running the Python app with MCP_PAT set via a .env file
GitHub Actions on pushes to main that SSHs into the instance and redeploys the app
Launch an Ubuntu or Amazon Linux 2023 EC2 instance.
Open inbound ports:
22 for SSH
80 for HTTP
443 for HTTPS
Install nginx and Python dependencies on the EC2 VM:
sudo apt-get update
sudo apt-get install -y python3 python3-venv python3-pip git nginxClone the repo:
cd /home/ubuntu
git clone git@github.com:Harshahi/ClinicalMCP.git
cd ClinicalMCP
python3 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .
cp .env.example .envUpdate .env with a real PAT and your public URL:
MCP_PAT=your-real-pat
MCP_ACCESS_URL=https://your-domain.example.com/mcp
MCP_PUBLIC_URL=https://your-domain.example.com
MCP_HOST=0.0.0.0
MCP_PORT=8000Configure NGINX to proxy traffic:
sudo tee /etc/nginx/conf.d/clinicalmcp.conf <<'EOF'
server {
listen 80;
server_name your-domain.example.com;
location / {
proxy_pass http://127.0.0.1:8000;
proxy_set_header Host $host;
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header X-Forwarded-Proto $scheme;
}
}
EOF
sudo nginx -t
sudo systemctl enable --now nginxCreate a systemd service:
sudo tee /etc/systemd/system/clinicalmcp.service <<'EOF'
[Unit]
Description=ClinicalMCP Server
After=network.target
[Service]
WorkingDirectory=/home/ubuntu/ClinicalMCP
EnvironmentFile=/home/ubuntu/ClinicalMCP/.env
ExecStart=/home/ubuntu/ClinicalMCP/.venv/bin/python -m mcp_clinical.server
Restart=always
RestartSec=5
User=ubuntu
Group=ubuntu
[Install]
WantedBy=multi-user.target
EOF
sudo systemctl daemon-reload
sudo systemctl enable --now clinicalmcp.service
sudo systemctl status clinicalmcp.service --no-pagerAdd the following repository secrets in GitHub:
EC2_HOST
EC2_USER
EC2_SSH_KEY
MCP_PAT
MCP_PUBLIC_URL
Example workflow:
name: deploy-to-ec2
on:
push:
branches: [main]
jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.13'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -e .
- name: Deploy to EC2
uses: appleboy/ssh-action@v1.1.0
with:
host: ${{ secrets.EC2_HOST }}
username: ${{ secrets.EC2_USER }}
key: ${{ secrets.EC2_SSH_KEY }}
script: |
set -e
cd /home/ubuntu/ClinicalMCP || git clone git@github.com:Harshahi/ClinicalMCP.git /home/ubuntu/ClinicalMCP
cd /home/ubuntu/ClinicalMCP
git pull origin main
python3 -m venv .venv
. .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -e .
cat > .env <<EOF
MCP_PAT=${{ secrets.MCP_PAT }}
MCP_ACCESS_URL=${{ secrets.MCP_PUBLIC_URL }}/mcp
MCP_PUBLIC_URL=${{ secrets.MCP_PUBLIC_URL }}
MCP_HOST=0.0.0.0
MCP_PORT=8000
EOF
sudo cp infra/clinicalmcp.service /etc/systemd/system/clinicalmcp.service
sudo systemctl daemon-reload
sudo systemctl restart clinicalmcp.service
sudo systemctl reload nginx || trueUse a public DNS name with HTTPS in front of the EC2 instance if you want a stable public URL.
If you want to terminate TLS at the EC2 load balancer or NGINX layer, install Certbot and configure 443 with Let’s Encrypt.
Keep the PAT in GitHub secrets and never commit it to source control.
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Clinical trial search and status from ClinicalTrials.gov
Search 36M+ PubMed biomedical articles and ClinicalTrials.gov studies.
Provide structured access to ClinicalTrials.gov data for searching, retrieving, and analyzing clin…
ClinicalTrials MCP — wraps ClinicalTrials.gov API v2 (free, no auth)
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