---

name: configuration-and-admin description: "Configure, start, validate, and troubleshoot Galaxy server/admin deployments, including galaxy.yml, jobs, object stores, dependency resolvers, and startup routing." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Galaxy Configuration And Admin

Use this sub-skill when a user needs help configuring or starting a Galaxy server, validating galaxy.yml, resolving config schema/startup errors, or planning admin changes around jobs, object stores, dependency resolvers, authentication, or Gravity process startup.

Start Here

1. Identify the active galaxy.yml; if missing, help the user copy or derive it from the bundled sample guidance rather than editing sample files in place.
2. Read configuration.md for the core file roles, top-level YAML shape, safe validation workflow, and bundled helper usage.
3. Read admin-operations.md for startup decisions, run.sh/Gravity concepts, job routing, object-store pointers, dependency resolvers, and authentication/config file routing.
4. Read troubleshooting.md when the symptom is a failed startup, YAML/schema error, missing config, path mistake, dependency resolver failure, or client/server confusion.

Bundled Helper

Run python scripts/validate_galaxy_config.py --config PATH to perform a safe read-only smoke check of a Galaxy YAML config. Add --sample PATH when comparing a copied sample or checking that a sample file is parseable. The helper does not start Galaxy, contact services, write files, install dependencies, or validate every Galaxy schema rule.

Routing Boundaries

• Use this sub-skill for galaxy.yml, startup, admin config files, job config pointers, dependency resolver configuration, authentication pointers, and high-level object-store references.
• Route object-store implementation details, data tables, dataset storage behavior, and storage migration planning to data-and-storage.
• Route API automation, admin API calls, scripted user/tool management, and client request examples to api-automation.
• Route tool XML, workflow authoring, Tool Shed behavior, and execution semantics to workflows-and-tools when present.
• Route JavaScript client build, npm/yarn, webpack/Vite, static asset, and UI development issues to web-client-development.

Safety Rules

• Treat database connections, object-store paths, job runner commands, dependency resolver paths, authentication providers, and proxy/socket settings as deployment-sensitive.
• Prefer dry-run/read-only checks first; do not create, migrate, delete, or move production database/storage content unless the user explicitly asks and provides a backup/rollback plan.
• Do not collect or print secrets from database URLs, OIDC/SAML settings, Vault config, cloud object-store credentials, or proxy authentication headers.
• Keep local development plans separate from production deployment plans; production usually needs an external database, proxy, process manager, logging, backups, and service monitoring beyond this sub-skill.