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    BioMCP-TS

    mcpkey · package
    io.github.yeyuan98/biomcp-ts · v1.4.3
    deploy just this

    Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.

    run it

    on your own machines, one way per deploy method
    generated from the record, not tested yet
    # once, as root:
# as_mcp DIR COMMAND...: runs COMMAND as the mcp user in DIR, its home, sandboxed as the
# units are: a package's install scripts can write to DIR only, as the server later can
as_mcp() {
  local dir="$1"; shift
  systemd-run --quiet --wait --pipe --collect --uid=mcp --gid=mcp \
    -p WorkingDirectory="$dir" -p Environment=HOME="$dir" -p ReadWritePaths="$dir" \
    -p NoNewPrivileges=true -p ProtectSystem=strict -p ProtectHome=true -p PrivateTmp=true \
    -- "$@" </dev/null
}
install -d -m 0750 -o mcp -g mcp /var/lib/mcp/biomcp-ts
# biomcp-ts: its packages, installed whole before its unit starts (no session installs)
# npx takes a half-installed tree for installed: a rerun starts them afresh
systemctl stop mcp-my-agent-biomcp-ts.service 2>/dev/null || true
as_mcp /var/lib/mcp/biomcp-ts rm -rf /var/lib/mcp/biomcp-ts/.npm/_npx
as_mcp /var/lib/mcp/biomcp-ts npx --yes [email protected] -- true
as_mcp /var/lib/mcp/biomcp-ts npx --yes --package=supergateway@4 -- true

#!/usr/bin/env bash
# biomcp-ts (io.github.yeyuan98/biomcp-ts), recipe baremetal (generated).
# Generated by Hub for toolset "my-agent"; started by mcp-my-agent-biomcp-ts.service.
set -euo pipefail
export HOST=127.0.0.1 PORT=8101
exec npx -y supergateway@4 --stdio 'npx -y [email protected]' --outputTransport streamableHttp --stateful --host 127.0.0.1 --port 8101 --streamableHttpPath /mcp --healthEndpoint /healthz

[Unit]
Description=MCP server biomcp-ts (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/biomcp-ts
WorkingDirectory=/var/lib/mcp/biomcp-ts
ExecStart=/opt/mcp/my-agent/bin/biomcp-ts.sh
Restart=on-failure
RestartSec=5
NoNewPrivileges=true
ProtectSystem=strict
ProtectHome=true
PrivateTmp=true
ReadWritePaths=/var/lib/mcp/biomcp-ts

[Install]
WantedBy=multi-user.target
    generated from the record, not tested yet
    docker run --rm -p 127.0.0.1:8101:8000 -e ANALYSIS_BIOWASM -e ANALYSIS_R -e DB_TYPE -e NCBI_API_KEY -e S2_API_KEY -e OPENFDA_API_KEY -e ONCOKB_TOKEN -e DISGENET_API_KEY node:22-alpine sh -c 'npx -y supergateway@4 --stdio '"'"'npx -y [email protected]'"'"' --outputTransport streamableHttp --stateful --host 0.0.0.0 --port 8000 --streamableHttpPath /mcp --healthEndpoint /healthz'
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T17:16:03+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:
  biomcp-ts:
    image: node:22-alpine
    command:
    - sh
    - -c
    - npx -y supergateway@4 --stdio 'npx -y [email protected]' --outputTransport streamableHttp --stateful
      --host 0.0.0.0 --port 8000 --streamableHttpPath /mcp --healthEndpoint /healthz
    ports:
    - 127.0.0.1:8101:8000
    volumes:
    - npm-cache:/root/.npm
    healthcheck:
      test:
      - CMD-SHELL
      - wget -qO- http://127.0.0.1:8000/healthz || exit 1
      interval: 30s
      timeout: 5s
      retries: 5
      start_period: 2m
    restart: unless-stopped
    environment:
      ANALYSIS_BIOWASM: ${ANALYSIS_BIOWASM}
      ANALYSIS_R: ${ANALYSIS_R}
      DB_TYPE: ${DB_TYPE}
      NCBI_API_KEY: ${NCBI_API_KEY}
      S2_API_KEY: ${S2_API_KEY}
      OPENFDA_API_KEY: ${OPENFDA_API_KEY}
      ONCOKB_TOKEN: ${ONCOKB_TOKEN}
      DISGENET_API_KEY: ${DISGENET_API_KEY}
volumes:
  npm-cache: {}
  uv-cache: {}
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T17:16:03+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: biomcp-ts
  namespace: mcp
  labels: &id001
    app: biomcp-ts
spec:
  replicas: 1
  selector:
    matchLabels: *id001
  template:
    metadata:
      labels: *id001
    spec:
      containers:
      - name: biomcp-ts
        image: node:22-alpine
        ports:
        - containerPort: 8000
          name: http
        env:
        - name: ANALYSIS_BIOWASM
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: ANALYSIS_BIOWASM
        - name: ANALYSIS_R
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: ANALYSIS_R
        - name: DB_TYPE
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: DB_TYPE
        - name: NCBI_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: NCBI_API_KEY
        - name: S2_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: S2_API_KEY
        - name: OPENFDA_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: OPENFDA_API_KEY
        - name: ONCOKB_TOKEN
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: ONCOKB_TOKEN
        - name: DISGENET_API_KEY
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: DISGENET_API_KEY
        args:
        - sh
        - -c
        - npx -y supergateway@4 --stdio 'npx -y [email protected]' --outputTransport streamableHttp --stateful
          --host 0.0.0.0 --port 8000 --streamableHttpPath /mcp --healthEndpoint /healthz
        readinessProbe:
          httpGet:
            path: /healthz
            port: http
          initialDelaySeconds: 10
---
apiVersion: v1
kind: Service
metadata:
  name: biomcp-ts
  namespace: mcp
spec:
  selector:
    app: biomcp-ts
  ports:
  - port: 8000
    targetPort: http
    name: http
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T17:16:03+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:
  biomcp-ts:
    enabled: true
    replicas: 1
    port: 8000
    path: /mcp
    container:
      name: biomcp-ts
      image: node:22-alpine
      ports:
      - containerPort: 8000
        name: http
      env:
      - name: ANALYSIS_BIOWASM
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: ANALYSIS_BIOWASM
      - name: ANALYSIS_R
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: ANALYSIS_R
      - name: DB_TYPE
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: DB_TYPE
      - name: NCBI_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: NCBI_API_KEY
      - name: S2_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: S2_API_KEY
      - name: OPENFDA_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: OPENFDA_API_KEY
      - name: ONCOKB_TOKEN
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: ONCOKB_TOKEN
      - name: DISGENET_API_KEY
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: DISGENET_API_KEY
      args:
      - sh
      - -c
      - npx -y supergateway@4 --stdio 'npx -y [email protected]' --outputTransport streamableHttp --stateful
        --host 0.0.0.0 --port 8000 --streamableHttpPath /mcp --healthEndpoint /healthz
      readinessProbe:
        httpGet:
          path: /healthz
          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: ANALYSIS_BIOWASM, ANALYSIS_R, DB_TYPE, NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY. 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
    npx -y [email protected]
# env: ANALYSIS_BIOWASM, ANALYSIS_R, DB_TYPE, NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY
    {
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "[email protected]"
      ],
      "env": {
        "ANALYSIS_BIOWASM": "${ANALYSIS_BIOWASM}",
        "ANALYSIS_R": "${ANALYSIS_R}",
        "DB_TYPE": "${DB_TYPE}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "S2_API_KEY": "${S2_API_KEY}",
        "OPENFDA_API_KEY": "${OPENFDA_API_KEY}",
        "ONCOKB_TOKEN": "${ONCOKB_TOKEN}",
        "DISGENET_API_KEY": "${DISGENET_API_KEY}"
      }
    }
  }
}
    #!/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 biomcp-ts -e "ANALYSIS_BIOWASM=${ANALYSIS_BIOWASM}" -e "ANALYSIS_R=${ANALYSIS_R}" -e "DB_TYPE=${DB_TYPE}" -e "NCBI_API_KEY=${NCBI_API_KEY}" -e "S2_API_KEY=${S2_API_KEY}" -e "OPENFDA_API_KEY=${OPENFDA_API_KEY}" -e "ONCOKB_TOKEN=${ONCOKB_TOKEN}" -e "DISGENET_API_KEY=${DISGENET_API_KEY}" -- npx -y [email protected]

    {
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "[email protected]"
      ],
      "env": {
        "ANALYSIS_BIOWASM": "${ANALYSIS_BIOWASM}",
        "ANALYSIS_R": "${ANALYSIS_R}",
        "DB_TYPE": "${DB_TYPE}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "S2_API_KEY": "${S2_API_KEY}",
        "OPENFDA_API_KEY": "${OPENFDA_API_KEY}",
        "ONCOKB_TOKEN": "${ONCOKB_TOKEN}",
        "DISGENET_API_KEY": "${DISGENET_API_KEY}"
      }
    }
  }
}
    {
  "servers": {
    "biomcp-ts": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "[email protected]"
      ],
      "env": {
        "ANALYSIS_BIOWASM": "${ANALYSIS_BIOWASM}",
        "ANALYSIS_R": "${ANALYSIS_R}",
        "DB_TYPE": "${DB_TYPE}",
        "NCBI_API_KEY": "${NCBI_API_KEY}",
        "S2_API_KEY": "${S2_API_KEY}",
        "OPENFDA_API_KEY": "${OPENFDA_API_KEY}",
        "ONCOKB_TOKEN": "${ONCOKB_TOKEN}",
        "DISGENET_API_KEY": "${DISGENET_API_KEY}"
      }
    }
  }
}
    name: my-agent
target: local
servers:
- hub: io.github.yeyuan98/biomcp-ts
    • 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.