Galaxy Repo Skill

Use this skill when a task involves the Galaxy scientific workflow platform repository: configuring or starting a Galaxy server, automating the Galaxy API, authoring tools or workflows, working with datatypes/storage, operating Tool Shed repositories, or developing the Vue/TypeScript web client.

Galaxy is a large package-centric Python and web monorepo. Start with the route map below, then read only the sub-skill and references that match the task.

Quick Start

• Read Repository Provenance before deciding whether this skill matches a current Galaxy checkout or needs refresh.
• Read Package Layout when the task depends on the monorepo, split packages, install modes, or import checks.
• Read Development and Testing when choosing focused Python, API, integration, framework, workflow, Selenium, Playwright, or client tests.
• Read Troubleshooting for cross-cutting install/import, package-layout, optional dependency, service, Node/client, and safety failures.
• Run python scripts/inspect_galaxy_environment.py --help for a safe environment/package-layout diagnostic helper.

Route Map

• Configuration and Admin: choose this for galaxy.yml, run.sh, Gravity/startup, config validation, jobs, dependency resolvers, admin configuration, and startup troubleshooting.
• API Automation: choose this for Galaxy HTTP API calls, API keys, histories, datasets, workflow import/invocation, OpenAPI orientation, API tests, and 401/403/400 debugging.
• Workflows and Tools: choose this for Galaxy tool XML/YAML, tool tests, workflow Format2 YAML, workflow framework tests, CWL surfaces, galaxy-tool-util CLIs, and dependency/mulled hints.
• Data and Storage: choose this for datatypes, sniffers, metadata, data managers, tool data tables, object stores, file sources, dataset storage, and storage cleanup safety.
• Tool Shed Operations: choose this for Tool Shed repositories, repository metadata reset, repository dependencies, installed Tool Shed tools, Tool Shed API scripts, shed_tool_conf.xml, and Whoosh indexes.
• Web Client Development: choose this for client/ pnpm workspace tasks, Vue/TypeScript code, Vitest, Pinia, MSW/OpenAPI mocks, Vite dev server, generated API-client package, and client build/test troubleshooting.

Common Decisions

• If the task names galaxy.yml, config samples, startup, database settings, jobs, dependency resolvers, or admin deployment, start with Configuration and Admin.
• If the task asks for curl, API keys, bioblend, OpenAPI, histories, datasets, or workflow invocation through HTTP, start with API Automation.
• If the task asks to write a Galaxy tool wrapper or workflow file, start with Workflows and Tools; use API Automation only when executing those artifacts through a running server.
• If the task mentions datatypes, sniffers, .loc, data managers, object stores, file sources, storage templates, cloud credentials, or cleanup scripts, start with Data and Storage.
• If the task mentions Tool Shed repository metadata, categories/users, installed repositories, repository dependencies, or Tool Shed search, start with Tool Shed Operations.
• If the task touches Vue components, TypeScript, pnpm, Vitest, MSW, generated API client, or Vite proxy settings, start with Web Client Development.

Install and Inspection Notes

Galaxy supports both a root checkout workflow and split packages under packages/. For coding-agent inspection, prefer scoped imports and split-package metadata over broad full-server installs unless the task explicitly needs a runnable Galaxy service.

Minimum orientation checks:

python - <<'PY'
import galaxy.version
print(galaxy.version.VERSION)
PY
python scripts/inspect_galaxy_environment.py --expected-version 26.2.dev0

The helper is read-only. It reports Python version, importability of representative Galaxy modules, installed split-package metadata when available, and common package-layout caveats. It does not start Galaxy, install dependencies, build the client, contact services, or mutate config/data.

Safety Boundaries

• Treat full Galaxy server startup, database migration, object-store migration, Tool Shed metadata reset, cloud storage tests, and client dependency installation as service- or environment-affecting operations; plan before running.
• Do not run cloud, credentialed, network-heavy, destructive cleanup, or long integration/Selenium/client build commands unless the user explicitly authorizes them and supplies the target environment.
• Prefer targeted unit/parser/help checks first; escalate to service-backed integration only after the generated route explains the risk and prerequisites.
• Keep API keys, database URLs, cloud credentials, OAuth secrets, and user data out of prompts, logs, and generated examples.

When to Refresh

Run refresh-repo-skill if the current Galaxy checkout commit, dirty source state, package version, split-package metadata, public API routes, tool-util CLIs, client workspace commands, or major evidence paths differ from Repository Provenance.