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Galaxy for Claude Code

This page sets up Claude Code with:

  • the galaxy-mcp server, so Claude can list histories, run tools, upload data and invoke workflows on your Galaxy server;
  • galaxy-skills, curated skills for using Galaxy (MCP tool surface, collections, user-defined tools, workflow reports, reproducibility);
  • galaxy-dev-skills, skills for building Galaxy (tool wrappers, Nextflow conversion, ToolShed revisions, track hubs, hub posts);
  • foundry-skills, the Galaxy Workflow Foundry's workflow-construction skills.

Prerequisites

  • Claude Code, a current release (claude --version).
  • uv on your PATH; the MCP server runs as uvx galaxy-mcp.
  • A Galaxy API key. See Getting a Galaxy API key.

Install

Inside Claude Code:

/plugin marketplace add galaxyproject/agentic-plugins
/plugin install galaxy-mcp@galaxyproject
/plugin install galaxy-skills@galaxyproject
/plugin install galaxy-dev-skills@galaxyproject
/plugin install foundry-skills@galaxyproject

Installing galaxy-mcp prompts for the Galaxy URL (default https://usegalaxy.org) and your API key. The key is stored in your system keychain, the URL in your user settings. Start a new session afterwards.

The same works from a terminal:

claude plugin marketplace add galaxyproject/agentic-plugins
claude plugin install galaxy-mcp@galaxyproject
claude plugin install galaxy-skills@galaxyproject
claude plugin install galaxy-dev-skills@galaxyproject
claude plugin install foundry-skills@galaxyproject

Install only what you need. galaxy-skills is the set for using Galaxy (MCP tool surface, collections, user-defined tools, workflow reports, reproducibility); galaxy-dev-skills is for building it (tool wrappers, Nextflow conversion, ToolShed revisions, track hubs, hub posts); foundry-skills adds 59 workflow-construction skills. Every installed skill costs context on every turn, so skip the sets you will not use.

Verify

  1. Run /mcp. A galaxy server should be listed under the galaxy-mcp plugin and connected.

  2. Ask:

    Connect to Galaxy and tell me who I am.

    Claude calls get_user and reports your username and the server version.

If something is off, run /galaxy-mcp:galaxy-connect; that skill walks Claude through diagnosing the connection.

Use the skills

Type / to see them. Plugin skills are namespaced, for example:

Invocation What it does
/galaxy-mcp:galaxy-connect Set up / verify / troubleshoot the Galaxy connection
/galaxy-skills:galaxy-integration Connect to an instance and choose how to drive it
/galaxy-skills:galaxy-mcp-reference The Galaxy MCP tool surface and its pitfalls
/galaxy-skills:collection-manipulation Filter, sort and restructure dataset collections
/galaxy-skills:udt-authoring Author user-defined tools (GalaxyUserTool YAML)
/galaxy-skills:workflow-reports Draft workflow report templates
/galaxy-skills:reproduciblify Rebuild a messy history as a clean, extractable analysis
/galaxy-dev-skills:tool-dev Create, test and update Galaxy tool wrappers
/galaxy-dev-skills:nf-to-galaxy Convert Nextflow processes and workflows
/galaxy-dev-skills:update-usegalaxy-tool Add or bump ToolShed revisions in usegalaxy-tools
/galaxy-dev-skills:trackhubs Publish UCSC track hubs and assembly hubs
/galaxy-dev-skills:hub-news-posts Write Galaxy Hub news posts
/foundry-skills:pipeline-nextflow-to-galaxy End-to-end Nextflow to Galaxy workflow conversion
/foundry-skills:discover-shed-tool Find and pin a Tool Shed wrapper

Claude also picks skills up on its own from your request; you do not have to invoke them by name.

Update

/plugin marketplace update galaxyproject
/plugin update galaxy-mcp@galaxyproject
/plugin update galaxy-skills@galaxyproject
/plugin update galaxy-dev-skills@galaxyproject
/plugin update foundry-skills@galaxyproject

Updating galaxy-mcp may prompt again for the Galaxy URL and API key.

The skills plugins are versioned by the date they were synced from upstream (a date such as 2026.9.17).

Change the Galaxy URL or key

Run /plugin configure galaxy-mcp@galaxyproject and edit the options, then start a new session. From a terminal, the same values can be set non-interactively:

claude plugin install galaxy-mcp@galaxyproject \
  --config galaxy_url=https://usegalaxy.org \
  --config galaxy_api_key="$GALAXY_API_KEY"

Export GALAXY_API_KEY first (see Getting a Galaxy API key); a key typed literally on the command line is stored in your shell history.

Uninstalling and reinstalling the plugin also prompts again:

/plugin uninstall galaxy-mcp@galaxyproject
/plugin install galaxy-mcp@galaxyproject

Alternatives

MCP server without the plugin. Register galaxy-mcp directly and pass the credentials yourself:

claude mcp add --scope user galaxy \
  -e GALAXY_URL=https://usegalaxy.org \
  -e GALAXY_API_KEY="$GALAXY_API_KEY" \
  -- uvx galaxy-mcp

Again the key comes from the exported variable (see Getting a Galaxy API key); typing it literally here stores it in your shell history.

Skills straight from upstream. Foundry publishes its own marketplace:

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Install either that or foundry-skills@galaxyproject, not both, or every Foundry skill appears twice. For galaxy-skills, cloning the repository into ~/.claude/skills/ also works:

git clone https://github.com/galaxyproject/galaxy-skills ~/.claude/skills/galaxy-skills

Troubleshooting

  • No galaxy server in /mcp: start a new session after installing; check uv --version.
  • Server fails to start: run uvx galaxy-mcp in a terminal to see the error. A first run downloads the package and needs network access.
  • "Plugin option galaxy_api_key isn't set" (in /mcp or the debug log): the install-time prompt was skipped; run /plugin configure galaxy-mcp@galaxyproject and fill in the options.
  • "Missing Galaxy URL and API key": the values did not reach the server; check /plugin configure galaxy-mcp@galaxyproject, or set GALAXY_URL / GALAXY_API_KEY in a project .env file.
  • "Provided API key is not valid": the key belongs to a different server or was revoked; create a new one and reinstall.