Galaxy for AI coding agents

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:

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.

This guide is generated from the Claude Code guide in agentic-plugins ; edit it there.

Codex CLI

This page sets up OpenAI Codex CLI with:

• the galaxy-mcp server, so Codex 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

• Codex CLI with plugin support (codex --version).
• uv on your PATH; the MCP server runs as uvx galaxy-mcp.
• A Galaxy API key. See Getting a Galaxy API key.

Set the credentials

Codex starts MCP servers with a minimal environment and forwards only the variables a server asks for. The galaxy-mcp plugin asks for GALAXY_URL and GALAXY_API_KEY, so export them in the shell that launches Codex (for example in ~/.zshrc or ~/.bashrc):

export GALAXY_URL="https://usegalaxy.org"
export GALAXY_API_KEY="paste-your-key-here"

A .env file with the same two lines in your project directory also works.

Install

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

Start a new Codex session afterwards. You can also browse and toggle the plugins with codex /plugins.

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. In a terminal, codex mcp list shows a galaxy server with GALAXY_URL and GALAXY_API_KEY (masked) and status enabled. Inside Codex, /mcp lists it too.

2. Ask:

   Connect to Galaxy and tell me who I am.

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

If something is off, type $galaxy-connect (or pick it from /skills) to have Codex diagnose the connection.

Use the skills

Type $ or run /skills to pick a skill, for example $galaxy-integration, $galaxy-mcp-reference, $collection-manipulation, $udt-authoring, $reproduciblify, and, if you installed galaxy-dev-skills, $tool-dev and $nf-to-galaxy. Codex also selects skills implicitly from their descriptions.

Codex scans plugin skill directories recursively, so the sub-skills nested under nf-to-galaxy and galaxy-integration (for example nf-process-to-galaxy-tool and jupyterlite-galaxy) are listed under their own names as well.

Update

codex plugin marketplace upgrade
codex plugin add galaxy-mcp@galaxyproject
codex plugin add galaxy-skills@galaxyproject
codex plugin add galaxy-dev-skills@galaxyproject
codex plugin add foundry-skills@galaxyproject

The first command refreshes the marketplace snapshot; re-adding a plugin installs the new version. galaxy-mcp reads the credentials from your environment, so no re-entry is needed. To remove a plugin:

codex plugin remove galaxy-skills@galaxyproject

Alternatives

MCP server without the plugin. In ~/.codex/config.toml, forwarding the variables from your shell instead of writing the key into the file:

[mcp_servers.galaxy]
command = "uvx"
args = ["galaxy-mcp"]
env_vars = ["GALAXY_URL", "GALAXY_API_KEY"]

or on the command line, taking the key from the same exported variable; a key typed literally here is stored in your shell history:

codex mcp add galaxy \
  --env GALAXY_URL=https://usegalaxy.org \
  --env GALAXY_API_KEY="$GALAXY_API_KEY" \
  -- uvx galaxy-mcp

Skills straight from upstream. Codex reads ~/.agents/skills/, so a clone works for galaxy-skills:

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

Foundry publishes its own Codex marketplace:

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

Install either that or foundry-skills@galaxyproject, not both.

Troubleshooting

• No galaxy server in /mcp: start a new session after installing; check uv --version.
• “Missing Galaxy URL and API key”: the variables are not exported in the shell that started Codex (GUI launchers often do not read ~/.zshrc). Use a project .env file, or the ~/.codex/config.toml form above (or codex mcp add ... --env ...).
• Server fails to start: run uvx galaxy-mcp in a terminal to see the error.
• “Provided API key is not valid”: the key belongs to a different server or was revoked.

This guide is generated from the Codex CLI guide in agentic-plugins ; edit it there.

Antigravity

This page sets up Google Antigravity (the agy CLI and the IDE, which share ~/.gemini/config/) with:

• the galaxy-mcp server, so the agent 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

• Antigravity CLI (agy --version) or the Antigravity IDE.
• uv on your PATH; the MCP server runs as uvx galaxy-mcp.
• git.
• A Galaxy API key. See Getting a Galaxy API key.

Set the credentials

Antigravity passes your shell environment to MCP servers, so export the two variables in the shell that launches agy (for example in ~/.zshrc or ~/.bashrc):

export GALAXY_URL="https://usegalaxy.org"
export GALAXY_API_KEY="paste-your-key-here"

A .env file with the same two lines in your project directory also works. ${VAR} placeholders inside mcp_config.json are not expanded, so do not try to reference the variables from the config file.

Install

Antigravity plugins are directories. Clone this repository and install the plugin directories you want:

git clone https://github.com/galaxyproject/agentic-plugins.git ~/.galaxy-agentic-plugins
agy plugin install ~/.galaxy-agentic-plugins/plugins/galaxy-mcp
agy plugin install ~/.galaxy-agentic-plugins/plugins/galaxy-skills
agy plugin install ~/.galaxy-agentic-plugins/plugins/galaxy-dev-skills
agy plugin install ~/.galaxy-agentic-plugins/plugins/foundry-skills

Each command copies the plugin into ~/.gemini/config/plugins/<name>/, where both the CLI and the IDE discover it. Start a new session afterwards.

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.

To scope a plugin to one workspace instead, copy its directory into <workspace>/.agents/plugins/ rather than running agy plugin install.

Verify

1. Type /mcp in the prompt to open the MCP manager; galaxy-mcp_galaxy (plugin servers are prefixed with the plugin name) should be running.

2. Ask:

   Connect to Galaxy and tell me who I am.

   The agent calls get_user and reports your username and the server version.

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

Use the skills

Run /skills to list them, or type / followed by the skill name, for example /galaxy-integration, /galaxy-mcp-reference, /collection-manipulation, /udt-authoring, /reproduciblify, /tool-dev, /nf-to-galaxy, /pipeline-nextflow-to-galaxy, /discover-shed-tool. The agent also picks skills up on its own from your request.

Antigravity lists only top-level skills. The nf-to-galaxy and galaxy-integration skills contain sub-skills in nested directories (for example nf-process-to-galaxy-tool); the parent skill links to them, so the agent reads them when needed even though they do not appear in /skills.

Update

git -C ~/.galaxy-agentic-plugins pull
agy plugin install ~/.galaxy-agentic-plugins/plugins/galaxy-mcp
agy plugin install ~/.galaxy-agentic-plugins/plugins/galaxy-skills
agy plugin install ~/.galaxy-agentic-plugins/plugins/galaxy-dev-skills
agy plugin install ~/.galaxy-agentic-plugins/plugins/foundry-skills

Reinstalling overwrites the installed copy. galaxy-mcp reads the credentials from your environment, so no re-entry is needed. agy plugin list shows what is installed; agy plugin uninstall <name> removes a plugin.

Alternatives

MCP server without the plugin. Register galaxy-mcp in your user-level mcp_config.json with the credentials inline:

agy mcp add --env GALAXY_URL=https://usegalaxy.org \
            --env GALAXY_API_KEY="$GALAXY_API_KEY" \
            galaxy uvx galaxy-mcp

The key comes from the variable exported above; typing it literally here stores it in your shell history.

Then install only the skills plugins, not galaxy-mcp, so the server is not registered twice.

Skills straight from upstream. Antigravity reads ~/.gemini/config/skills/<skill>/SKILL.md, so the galaxy-skills repository can be cloned there; each top-level skill directory becomes a skill:

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

Troubleshooting

• No galaxy-mcp_galaxy in /mcp: start a new session; run agy plugin list to confirm the plugin is installed; check uv --version.
• “Missing Galaxy URL and API key”: the variables are not exported in the shell that started agy (the IDE may not read ~/.zshrc). Use a project .env file, or the agy mcp add ... --env ... form above.
• Server fails to start: run uvx galaxy-mcp in a terminal to see the error.
• “Provided API key is not valid”: the key belongs to a different server or was revoked.

This guide is generated from the Antigravity guide in agentic-plugins ; edit it there.

Pi

This page sets up Pi (the pi coding agent) with:

• the galaxy-mcp server, so the agent 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.

Looking for a complete Galaxy research assistant built on Pi? See Loom instead; this page is for adding Galaxy to a plain Pi installation.

Prerequisites

• Pi (pi --version) and Node.js.
• uv on your PATH; the MCP server runs as uvx galaxy-mcp.
• A Galaxy API key. See Getting a Galaxy API key.

Set the credentials

Pi’s MCP adapter passes your shell environment to MCP servers, so export the two variables in the shell that launches pi (for example in ~/.zshrc or ~/.bashrc):

export GALAXY_URL="https://usegalaxy.org"
export GALAXY_API_KEY="paste-your-key-here"

A .env file with the same two lines in your project directory also works.

Install

Pi has no built-in MCP support; the pi-mcp-adapter package adds it and reads the MCP configuration shipped in this package.

pi install npm:pi-mcp-adapter
pi install git:github.com/galaxyproject/agentic-plugins

Restart Pi afterwards. The second command clones this repository under ~/.pi/agent/git/ and registers its skills and MCP configuration from the pi section of package.json. Use pi install -l ... to install into the current project’s .pi/settings.json instead of your user settings.

Verify

1. Run /mcp inside Pi. A server named galaxyproject_agentic_plugins__galaxy should be listed (the adapter prefixes package-provided servers with the package name). It connects lazily on first use.

2. Ask:

   Connect to Galaxy and tell me who I am.

   The agent calls get_user through the adapter’s mcp tool and reports your username and server version.

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

Use the skills

Skills register as /skill:<name> commands, for example /skill:galaxy-integration, /skill:galaxy-mcp-reference, /skill:collection-manipulation, /skill:udt-authoring, /skill:reproduciblify, /skill:tool-dev, /skill:nf-to-galaxy, /skill:pipeline-nextflow-to-galaxy, /skill:discover-shed-tool. The agent also loads skills on its own when a request matches a description.

The package carries every skill set: galaxy-skills (using Galaxy), galaxy-dev-skills (tool wrappers, Nextflow conversion, ToolShed, hubs) and foundry-skills (59 workflow-construction skills). To leave out the sets you do not use, filter the package in ~/.pi/agent/settings.json (or .pi/settings.json):

{
  "packages": [
    "npm:pi-mcp-adapter",
    {
      "source": "git:github.com/galaxyproject/agentic-plugins",
      "skills": ["!plugins/foundry-skills/**", "!plugins/galaxy-dev-skills/**"]
    }
  ]
}

pi config toggles individual skills interactively.

Update

pi update --extensions

refreshes installed packages. To pin a release, install a tag: pi install git:github.com/galaxyproject/agentic-plugins@<tag>, where <tag> is a release from the releases page.

Alternatives

MCP server without this package. With pi-mcp-adapter installed, put a standard MCP file in your project (.mcp.json) or globally (~/.config/mcp/mcp.json):

{
  "mcpServers": {
    "galaxy": {
      "command": "uvx",
      "args": ["galaxy-mcp"],
      "env": {
        "GALAXY_URL": "https://usegalaxy.org",
        "GALAXY_API_KEY": "paste-your-key-here"
      }
    }
  }
}

Skills straight from upstream. Pi reads ~/.agents/skills/ recursively:

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

Troubleshooting

• No Galaxy server in /mcp: confirm both packages are listed by pi list, restart Pi, and check uv --version.
• “Missing Galaxy URL and API key”: the variables are not exported in the shell that started pi. Use a project .env file, or the .mcp.json form above.
• Server fails to start: run uvx galaxy-mcp in a terminal to see the error.
• “Provided API key is not valid”: the key belongs to a different server or was revoked.

This guide is generated from the Pi guide in agentic-plugins ; edit it there.

Claude Desktop

This page installs the galaxy-mcp server into Claude Desktop as a one-click bundle, so Claude can list your histories, upload and inspect datasets, search and run tools, and invoke workflows on your Galaxy server. No terminal needed.

Skills (galaxy-skills, galaxy-dev-skills, foundry-skills) are for coding agents and do not apply to Claude Desktop.

Prerequisites

• Claude Desktop for macOS or Windows (Linux builds also support bundles).
• A Galaxy API key. See Getting a Galaxy API key.

Python is not required: the bundle uses Claude Desktop’s built-in uv runtime, which downloads Python and installs galaxy-mcp from PyPI on first start.

Install

1. Download galaxy-mcp.mcpb from the latest release.
2. Open it with Claude Desktop (double-click, or drag it onto the Claude window; you can also use Settings > Extensions > Advanced settings > Install Extension…).
3. In the install dialog, fill in:
   • Galaxy URL: your server, default https://usegalaxy.org.
   • Galaxy API key: the key from User > Preferences > Manage API Key. It is stored in your system keychain.
4. Click Install. The first start takes a minute while galaxy-mcp is downloaded.

Verify

Start a new chat and ask:

Connect to Galaxy and tell me who I am.

Claude calls get_user and reports your username and the server version. Then try:

Show my three most recent histories.

Change the URL or key

Settings > Extensions > Galaxy > Configure. Restart the chat afterwards.

Update

Download the newer .mcpb from the releases page and open it; Claude Desktop replaces the installed version and keeps your settings.

Manual alternative (no bundle)

Add the server to claude_desktop_config.json (Settings > Developer > Edit Config). This requires uv on your PATH:

{
  "mcpServers": {
    "galaxy": {
      "command": "uvx",
      "args": ["galaxy-mcp"],
      "env": {
        "GALAXY_URL": "https://usegalaxy.org",
        "GALAXY_API_KEY": "paste-your-key-here"
      }
    }
  }
}

Troubleshooting

• Extension shows an error after install: open Settings > Extensions > Galaxy and check the log; the first start needs network access to fetch Python and galaxy-mcp.
• “Provided API key is not valid”: the key belongs to a different server or was revoked; create a new one and update it under Configure.
• “Missing Galaxy URL and API key”: the configuration dialog was skipped; open Configure and fill both fields.
• Slow first response: galaxy-mcp starts on demand; later calls are fast.

This guide is generated from the Claude Desktop guide in agentic-plugins ; edit it there.