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DimensionGalaxy MCP ServerMCP server for the Galaxy bioinformatics platformMartinLoop MCP ServerAn independent control layer that gives AI coding agents budgets, brakes, and receipts
FMRS61 / 100 · C79 / 100 · B
Reliability9 / 2012 / 20
Security and permissions13 / 2018 / 20
Maintenance12 / 2016 / 20
Documentation14 / 2018 / 20
Setup experience13 / 2015 / 20
Best for
  • Bioinformatics researchers who want AI assistants to operate the Galaxy platform
  • Galaxy instance administrators and regular Galaxy users
  • Teams automating analysis workflows
  • Engineering teams scaling AI coding agents while controlling spend
  • Platform teams that need auditable, rollback-aware agent execution records
  • Organizations using multiple agents (Claude, Codex, Gemini) under one governed flow
Not for
  • Users not on the Galaxy platform
  • Environments without a Galaxy URL and API key
  • General-purpose bioinformatics outside Galaxy
  • Developers who just want a simple code-completion helper without run governance
  • Teams unwilling to accept local JSONL run records with HMAC signing
  • Environments without a supported adapter (Claude/Codex/Gemini CLIs, direct provider, or verifier-only)
Required permissions
  • Requires the target Galaxy instance URL (GALAXY_URL, required)
  • Requires a Galaxy API key (GALAXY_API_KEY, required and secret; may be omitted when using OAuth)
  • OAuth mode requires a session secret (GALAXY_MCP_SESSION_SECRET) and public URL (GALAXY_MCP_PUBLIC_URL)
  • Read/write access to the configured repo root (writable scope restrictable via --allow-path/--deny-path)
  • Ability to invoke the chosen agent CLI (Claude/Codex/Gemini, etc.) and its underlying model account
  • Local disk writes for run records, receipts, and share outputs (share/run-receipt., etc.)
  • Execution of user-configured verifier commands (e.g. npm test)
Risks and side effects
  • The API key is a sensitive credential; leakage grants others access to your Galaxy account and analyses
  • Tools and workflows executed by the AI consume Galaxy compute resources
  • Remote HTTP deployment exposes a network port and requires careful OAuth and session-secret configuration
  • Verifier commands are executed; poorly chosen verifier commands carry security risk despite preflight policy checks
  • Cost and token figures may be estimates (labeled with provenance) and should not be treated as settled accounting
  • Receipt integrity must be verified before use as trustworthy evidence; missing rollback evidence is flagged as EVIDENCE_BOUNDARY
  • Policy defaults come from martin.config.yaml and can be overridden by CLI flags; misconfiguration can loosen safety boundaries
Supported clientsClaude DesktopClaude Code, Codex, Gemini CLI, Cursor, VS Code, GitHub Copilot, Continue
Tools00