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    Cytoscape Desktop MCP

    mcpkey · package
    io.github.cytoscape/cytoscape-desktop-mcp-bridge · v1.0.3
    deploy just this

    Drive a running Cytoscape Desktop to load, lay out, and style biological networks.

    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/cytoscape-desktop-mcp-bridge
# cytoscape-desktop-mcp-bridge: 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-cytoscape-desktop-mcp-bridge.service 2>/dev/null || true
as_mcp /var/lib/mcp/cytoscape-desktop-mcp-bridge rm -rf /var/lib/mcp/cytoscape-desktop-mcp-bridge/.npm/_npx
as_mcp /var/lib/mcp/cytoscape-desktop-mcp-bridge npx --yes --package=@cytoscape/[email protected] -- true
as_mcp /var/lib/mcp/cytoscape-desktop-mcp-bridge npx --yes --package=supergateway@4 -- true

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

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

[Install]
WantedBy=multi-user.target
    generated from the record, not tested yet
    docker run --rm -p 127.0.0.1:8101:8000 -e CYREST_PORT node:22-alpine sh -c 'npx -y supergateway@4 --stdio '"'"'npx -y @cytoscape/[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" (2026-10-18T21:36:52+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:
  cytoscape-desktop-mcp-bridge:
    image: node:22-alpine
    command:
    - sh
    - -c
    - npx -y supergateway@4 --stdio 'npx -y @cytoscape/[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:
      CYREST_PORT: ${CYREST_PORT}
volumes:
  npm-cache: {}
  uv-cache: {}
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T21:36:52+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: cytoscape-desktop-mcp-bridge
  namespace: mcp
  labels: &id001
    app: cytoscape-desktop-mcp-bridge
spec:
  replicas: 1
  selector:
    matchLabels: *id001
  template:
    metadata:
      labels: *id001
    spec:
      containers:
      - name: cytoscape-desktop-mcp-bridge
        image: node:22-alpine
        ports:
        - containerPort: 8000
          name: http
        env:
        - name: CYREST_PORT
          valueFrom:
            secretKeyRef:
              name: mcp-credentials
              key: CYREST_PORT
        args:
        - sh
        - -c
        - npx -y supergateway@4 --stdio 'npx -y @cytoscape/[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: cytoscape-desktop-mcp-bridge
  namespace: mcp
spec:
  selector:
    app: cytoscape-desktop-mcp-bridge
  ports:
  - port: 8000
    targetPort: http
    name: http
    generated from the record, not tested yet
    # Generated by Hub for toolset "my-agent" (2026-10-18T21:36:52+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:
  cytoscape-desktop-mcp-bridge:
    enabled: true
    replicas: 1
    port: 8000
    path: /mcp
    container:
      name: cytoscape-desktop-mcp-bridge
      image: node:22-alpine
      ports:
      - containerPort: 8000
        name: http
      env:
      - name: CYREST_PORT
        valueFrom:
          secretKeyRef:
            name: mcp-credentials
            key: CYREST_PORT
      args:
      - sh
      - -c
      - npx -y supergateway@4 --stdio 'npx -y @cytoscape/[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: CYREST_PORT. 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 @cytoscape/[email protected]
# env: CYREST_PORT
    {
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "${CYREST_PORT}"
      }
    }
  }
}
    #!/usr/bin/env bash
# Registers every server with Claude Code (run once; `claude mcp list` to check).
set -euo pipefail
set -a; [ -f .env ] && source .env; set +a
claude mcp add cytoscape-desktop-mcp-bridge -e "CYREST_PORT=${CYREST_PORT}" -- npx -y @cytoscape/[email protected]

    {
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "${CYREST_PORT}"
      }
    }
  }
}
    {
  "servers": {
    "cytoscape-desktop-mcp-bridge": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "${CYREST_PORT}"
      }
    }
  }
}
    name: my-agent
target: local
servers:
- hub: io.github.cytoscape/cytoscape-desktop-mcp-bridge
    • 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.