name: tool-shed-operations
description: "Operate Galaxy Tool Shed repositories, repository metadata,
installed Tool Shed tools, Tool Shed APIs, and publishing/install
troubleshooting safely."
disable-model-invocation: true
metadata:
disco-role: operating
license: NOASSERTION
Galaxy Tool Shed Operations
Use this sub-skill when a task involves Tool Shed repository installation or publishing, repository metadata reset/regeneration, repository dependencies, installed Tool Shed repositories, Tool Shed API scripts, test shed bootstrapping, shed_tool_conf.xml, or Tool Shed Whoosh search indexes.
Start Here
- Read Tool Shed Workflows for repository installation, metadata reset, repository dependencies, installed-repository state, and search-index workflows.
- Read API And Scripts for Tool Shed API surfaces, bundled dry-run planning, legacy script behavior, and service-required scripts.
- Read Troubleshooting when installs, metadata, repository dependencies, permissions, search, or reset operations fail.
- Use
python scripts/tool_shed_api_plan.py --help to draft safe plans for categories, users, metadata reset, install checks, and Whoosh-index work without contacting a server by default.
Routing Boundaries
- Stay here for Tool Shed repositories, Tool Shed-side categories/users, repository metadata,
repository_dependencies.xml, installed Tool Shed repository state, Tool Shed search indexes, and shed_tool_conf.xml effects.
- Use Workflows And Tools for local tool XML, tool tests, workflow YAML, and wrapper authoring before a repository is published.
- Use API Automation for generic Galaxy API authentication, histories, datasets, workflows, OpenAPI inspection, and non-Tool-Shed API automation.
- Use Configuration And Admin for
galaxy.yml, server startup, process management, and general admin configuration around shed config files.
Safety Defaults
- Treat every non-local Tool Shed or Galaxy URL as production-like until the user confirms it is disposable or staging.
- Prefer dry-run plans and metadata previews before write actions; do not create users/categories, reset production metadata, reinstall repositories, or rebuild indexes without explicit user approval.
- Do not print or persist API keys; pass secrets through environment variables and redact them in logs or generated command plans.
- Distinguish Tool Shed server APIs from Galaxy server APIs: Tool Shed APIs manage repositories/categories/users, while Galaxy APIs manage installed Tool Shed repositories inside a Galaxy instance.