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    tooluniverse

    mcpkey · package
    io.github.mims-harvard/tooluniverse · v1.5.7
    deploy just this

    2,700+ scientific tools for AI scientists: life science, research, literature, and more.

    run it

    on your own machines, one way per deploy method
    generated from the record, not tested yet
    #!/usr/bin/env bash
# tooluniverse (io.github.mims-harvard/tooluniverse), recipe baremetal (generated).
# Generated by Hub for toolset "my-agent"; started by mcp-my-agent-tooluniverse.service.
set -euo pipefail
export HOST=127.0.0.1 PORT=8101
exec uvx mcp-proxy --host 127.0.0.1 --port 8101 --pass-environment -- uvx tooluniverse==1.5.7

[Unit]
Description=MCP server tooluniverse (toolset my-agent), generated by Hub
After=network-online.target
Wants=network-online.target

[Service]
Type=simple
User=mcp
Group=mcp
EnvironmentFile=/etc/mcp/my-agent.env
Environment=HOME=/var/lib/mcp/tooluniverse
WorkingDirectory=/var/lib/mcp/tooluniverse
ExecStart=/opt/mcp/my-agent/bin/tooluniverse.sh
Restart=on-failure
RestartSec=5
NoNewPrivileges=true
ProtectSystem=strict
ProtectHome=true
PrivateTmp=true
ReadWritePaths=/var/lib/mcp/tooluniverse

[Install]
WantedBy=multi-user.target
    generated from the record, not tested yet
    docker run --rm -p 127.0.0.1:8101:8000 -e OPENAI_API_KEY -e ANTHROPIC_API_KEY -e GEMINI_API_KEY -e OPENROUTER_API_KEY -e AZURE_OPENAI_API_KEY -e HF_TOKEN -e NCBI_API_KEY -e SEMANTIC_SCHOLAR_API_KEY -e BIOGRID_API_KEY -e DISGENET_API_KEY -e OMIM_API_KEY -e ONCOKB_API_TOKEN -e NVIDIA_API_KEY -e USPTO_API_KEY -e UMLS_API_KEY -e BRENDA_EMAIL -e BRENDA_PASSWORD ghcr.io/astral-sh/uv:python3.12-bookworm-slim sh -c 'uvx mcp-proxy --host 0.0.0.0 --port 8000 --pass-environment -- uvx tooluniverse==1.5.7'
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T12:56:56+00:00).
# Each package server runs behind a stdio->HTTP bridge and listens on localhost only.
#   cp .env.example .env    # fill the ${VAR}s
#   docker compose up -d && bash smoke.sh
# Remote servers are not here: clients reach them directly (see clients/).
name: mcp-my-agent
services:
  tooluniverse:
    image: ghcr.io/astral-sh/uv:python3.12-bookworm-slim
    command:
    - sh
    - -c
    - uvx mcp-proxy --host 0.0.0.0 --port 8000 --pass-environment -- uvx tooluniverse==1.5.7
    ports:
    - 127.0.0.1:8101:8000
    volumes:
    - uv-cache:/root/.cache/uv
    healthcheck:
      test:
      - CMD
      - python3
      - -c
      - import urllib.request; urllib.request.urlopen('http://127.0.0.1:8000/status')
      interval: 30s
      timeout: 5s
      retries: 5
      start_period: 2m
    restart: unless-stopped
    environment:
      OPENAI_API_KEY: ${OPENAI_API_KEY}
      ANTHROPIC_API_KEY: ${ANTHROPIC_API_KEY}
      GEMINI_API_KEY: ${GEMINI_API_KEY}
      OPENROUTER_API_KEY: ${OPENROUTER_API_KEY}
      AZURE_OPENAI_API_KEY: ${AZURE_OPENAI_API_KEY}
      HF_TOKEN: ${HF_TOKEN}
      NCBI_API_KEY: ${NCBI_API_KEY}
      SEMANTIC_SCHOLAR_API_KEY: ${SEMANTIC_SCHOLAR_API_KEY}
      BIOGRID_API_KEY: ${BIOGRID_API_KEY}
      DISGENET_API_KEY: ${DISGENET_API_KEY}
      OMIM_API_KEY: ${OMIM_API_KEY}
      ONCOKB_API_TOKEN: ${ONCOKB_API_TOKEN}
      NVIDIA_API_KEY: ${NVIDIA_API_KEY}
      USPTO_API_KEY: ${USPTO_API_KEY}
      UMLS_API_KEY: ${UMLS_API_KEY}
      BRENDA_EMAIL: ${BRENDA_EMAIL}
      BRENDA_PASSWORD: ${BRENDA_PASSWORD}
volumes:
  npm-cache: {}
  uv-cache: {}
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T12:56:56+00:00).
#   kubectl create namespace mcp
#   kubectl -n mcp create secret generic mcp-credentials --from-env-file=.env
#   kubectl apply -f kubernetes.yaml
# Services are cluster-internal: <name>.mcp.svc.cluster.local:8000/mcp. Put an ingress
# with auth in front before exposing any of them.
apiVersion: v1
kind: Namespace
metadata:
  name: mcp
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: tooluniverse
  namespace: mcp
  labels: &id001
    app: tooluniverse
spec:
  replicas: 1
  selector:
    matchLabels: *id001
  template:
    metadata:
      labels: *id001
    spec:
      containers:
      - name: tooluniverse
        image: ghcr.io/astral-sh/uv:python3.12-bookworm-slim
        ports:
        - containerPort: 8000
          name: http
        env:
        - name: OPENAI_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: OPENAI_API_KEY
        - name: ANTHROPIC_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: ANTHROPIC_API_KEY
        - name: GEMINI_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: GEMINI_API_KEY
        - name: OPENROUTER_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: OPENROUTER_API_KEY
        - name: AZURE_OPENAI_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: AZURE_OPENAI_API_KEY
        - name: HF_TOKEN
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: HF_TOKEN
        - name: NCBI_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: NCBI_API_KEY
        - name: SEMANTIC_SCHOLAR_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: SEMANTIC_SCHOLAR_API_KEY
        - name: BIOGRID_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: BIOGRID_API_KEY
        - name: DISGENET_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: DISGENET_API_KEY
        - name: OMIM_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: OMIM_API_KEY
        - name: ONCOKB_API_TOKEN
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: ONCOKB_API_TOKEN
        - name: NVIDIA_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: NVIDIA_API_KEY
        - name: USPTO_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: USPTO_API_KEY
        - name: UMLS_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: UMLS_API_KEY
        - name: BRENDA_EMAIL
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: BRENDA_EMAIL
        - name: BRENDA_PASSWORD
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: BRENDA_PASSWORD
        command:
        - sh
        - -c
        - uvx mcp-proxy --host 0.0.0.0 --port 8000 --pass-environment -- uvx tooluniverse==1.5.7
        readinessProbe:
          httpGet:
            path: /status
            port: http
          initialDelaySeconds: 10
---
apiVersion: v1
kind: Service
metadata:
  name: tooluniverse
  namespace: mcp
spec:
  selector:
    app: tooluniverse
  ports:
  - port: 8000
    targetPort: http
    name: http
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T12:56:56+00:00).
# Credentials come from the Secret 'mcp-credentials' (kubectl create secret generic ... --from-env-file=.env).
# Each server under `servers` is one Deployment + Service; the keys after it configure
# upstream charts a worker verified.
servers:
  tooluniverse:
    enabled: true
    replicas: 1
    port: 8000
    path: /mcp
    container:
      name: tooluniverse
      image: ghcr.io/astral-sh/uv:python3.12-bookworm-slim
      ports:
      - containerPort: 8000
        name: http
      env:
      - name: OPENAI_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: OPENAI_API_KEY
      - name: ANTHROPIC_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: ANTHROPIC_API_KEY
      - name: GEMINI_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: GEMINI_API_KEY
      - name: OPENROUTER_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: OPENROUTER_API_KEY
      - name: AZURE_OPENAI_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: AZURE_OPENAI_API_KEY
      - name: HF_TOKEN
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: HF_TOKEN
      - name: NCBI_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: NCBI_API_KEY
      - name: SEMANTIC_SCHOLAR_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: SEMANTIC_SCHOLAR_API_KEY
      - name: BIOGRID_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: BIOGRID_API_KEY
      - name: DISGENET_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: DISGENET_API_KEY
      - name: OMIM_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: OMIM_API_KEY
      - name: ONCOKB_API_TOKEN
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: ONCOKB_API_TOKEN
      - name: NVIDIA_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: NVIDIA_API_KEY
      - name: USPTO_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: USPTO_API_KEY
      - name: UMLS_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: UMLS_API_KEY
      - name: BRENDA_EMAIL
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: BRENDA_EMAIL
      - name: BRENDA_PASSWORD
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: BRENDA_PASSWORD
      command:
      - sh
      - -c
      - uvx mcp-proxy --host 0.0.0.0 --port 8000 --pass-environment -- uvx tooluniverse==1.5.7
      readinessProbe:
        httpGet:
          path: /status
          port: http
        initialDelaySeconds: 10

# helm install my-agent helm/my-agent -n mcp

    in the cloud

    one click: the provider's deploy form opens filled in, in your own account
    koyeb
    deploy to koyeb

    The form opens with CHANGE_ME for each value you supply: OPENAI_API_KEY, ANTHROPIC_API_KEY, GEMINI_API_KEY, OPENROUTER_API_KEY, AZURE_OPENAI_API_KEY, HF_TOKEN, NCBI_API_KEY, SEMANTIC_SCHOLAR_API_KEY, BIOGRID_API_KEY, DISGENET_API_KEY, OMIM_API_KEY, ONCOKB_API_TOKEN, NVIDIA_API_KEY, USPTO_API_KEY, UMLS_API_KEY, BRENDA_EMAIL, BRENDA_PASSWORD. Fill them in before you deploy.

    Clients connect to the service's https://…koyeb.app address plus /mcp.

    azure
    deploy to azuretemplate

    A Container Apps environment with one app per server, each with HTTPS ingress and one replica. The portal asks for each value you supply as a secure parameter; the deployment's outputs list the endpoints.

    connect to it

    copy what your client needs
    uvx tooluniverse==1.5.7
# env: OPENAI_API_KEY, ANTHROPIC_API_KEY, GEMINI_API_KEY, OPENROUTER_API_KEY, AZURE_OPENAI_API_KEY, HF_TOKEN, NCBI_API_KEY, SEMANTIC_SCHOLAR_API_KEY, BIOGRID_API_KEY, DISGENET_API_KEY, OMIM_API_KEY, ONCOKB_API_TOKEN, NVIDIA_API_KEY, USPTO_API_KEY, UMLS_API_KEY, BRENDA_EMAIL, BRENDA_PASSWORD
    {
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": [
        "tooluniverse==1.5.7"
      ],
      "env": {
        "OPENAI_API_KEY": "${OPENAI_API_KEY}",
        "ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
        "GEMINI_API_KEY": "${GEMINI_API_KEY}",
        "OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
        "AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
        "HF_TOKEN": "${HF_TOKEN}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
        "BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
        "DISGENET_API_KEY": "${DISGENET_API_KEY}",
        "OMIM_API_KEY": "${OMIM_API_KEY}",
        "ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
        "NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
        "USPTO_API_KEY": "${USPTO_API_KEY}",
        "UMLS_API_KEY": "${UMLS_API_KEY}",
        "BRENDA_EMAIL": "${BRENDA_EMAIL}",
        "BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
      }
    }
  }
}
    #!/usr/bin/env bash
# Registers every server with Claude Code (run once; `claude mcp list` to check).
set -euo pipefail
set -a; [ -f .env ] && source .env; set +a
claude mcp add tooluniverse -e "OPENAI_API_KEY=${OPENAI_API_KEY}" -e "ANTHROPIC_API_KEY=${ANTHROPIC_API_KEY}" -e "GEMINI_API_KEY=${GEMINI_API_KEY}" -e "OPENROUTER_API_KEY=${OPENROUTER_API_KEY}" -e "AZURE_OPENAI_API_KEY=${AZURE_OPENAI_API_KEY}" -e "HF_TOKEN=${HF_TOKEN}" -e "NCBI_API_KEY=${NCBI_API_KEY}" -e "SEMANTIC_SCHOLAR_API_KEY=${SEMANTIC_SCHOLAR_API_KEY}" -e "BIOGRID_API_KEY=${BIOGRID_API_KEY}" -e "DISGENET_API_KEY=${DISGENET_API_KEY}" -e "OMIM_API_KEY=${OMIM_API_KEY}" -e "ONCOKB_API_TOKEN=${ONCOKB_API_TOKEN}" -e "NVIDIA_API_KEY=${NVIDIA_API_KEY}" -e "USPTO_API_KEY=${USPTO_API_KEY}" -e "UMLS_API_KEY=${UMLS_API_KEY}" -e "BRENDA_EMAIL=${BRENDA_EMAIL}" -e "BRENDA_PASSWORD=${BRENDA_PASSWORD}" -- uvx tooluniverse==1.5.7

    {
  "mcpServers": {
    "tooluniverse": {
      "command": "uvx",
      "args": [
        "tooluniverse==1.5.7"
      ],
      "env": {
        "OPENAI_API_KEY": "${OPENAI_API_KEY}",
        "ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
        "GEMINI_API_KEY": "${GEMINI_API_KEY}",
        "OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
        "AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
        "HF_TOKEN": "${HF_TOKEN}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
        "BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
        "DISGENET_API_KEY": "${DISGENET_API_KEY}",
        "OMIM_API_KEY": "${OMIM_API_KEY}",
        "ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
        "NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
        "USPTO_API_KEY": "${USPTO_API_KEY}",
        "UMLS_API_KEY": "${UMLS_API_KEY}",
        "BRENDA_EMAIL": "${BRENDA_EMAIL}",
        "BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
      }
    }
  }
}
    {
  "servers": {
    "tooluniverse": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "tooluniverse==1.5.7"
      ],
      "env": {
        "OPENAI_API_KEY": "${OPENAI_API_KEY}",
        "ANTHROPIC_API_KEY": "${ANTHROPIC_API_KEY}",
        "GEMINI_API_KEY": "${GEMINI_API_KEY}",
        "OPENROUTER_API_KEY": "${OPENROUTER_API_KEY}",
        "AZURE_OPENAI_API_KEY": "${AZURE_OPENAI_API_KEY}",
        "HF_TOKEN": "${HF_TOKEN}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "SEMANTIC_SCHOLAR_API_KEY": "${SEMANTIC_SCHOLAR_API_KEY}",
        "BIOGRID_API_KEY": "${BIOGRID_API_KEY}",
        "DISGENET_API_KEY": "${DISGENET_API_KEY}",
        "OMIM_API_KEY": "${OMIM_API_KEY}",
        "ONCOKB_API_TOKEN": "${ONCOKB_API_TOKEN}",
        "NVIDIA_API_KEY": "${NVIDIA_API_KEY}",
        "USPTO_API_KEY": "${USPTO_API_KEY}",
        "UMLS_API_KEY": "${UMLS_API_KEY}",
        "BRENDA_EMAIL": "${BRENDA_EMAIL}",
        "BRENDA_PASSWORD": "${BRENDA_PASSWORD}"
      }
    }
  }
}
    name: my-agent
target: local
servers:
- hub: io.github.mims-harvard/tooluniverse
    • not probed yet: tools unpinned, ingest lists them

    tools

    Not probed yetThe tools appear once the hub or its worker has listed this entry. Running it still works: your client lists them on first start.