galaxy-mcp — Claude Code MCP server: what it does, how to install
Links AI clients with the Galaxy bioinformatics platform. Run analysis tools, manage histories, and track complex scientific pipelines right from the chat.
claude mcp add galaxy-mcp -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcpWhat galaxy-mcp does
This server exposes Galaxy bioinformatics instances to MCP clients via standard I/O or HTTP streaming. It provides tools to search the platform catalog, inspect parameter schemas, and execute computational jobs. Clients can also manage histories, handle dataset collections, and import validated workflows from the Intergalactic Workflow Commission.
The environment requires an active GALAXY_URL alongside a valid GALAXY_API_KEY for authentication. Without these credentials, requests to schedule jobs or fetch data will fail immediately. An optional code-mode flag collapses the catalog into three meta-tools to preserve context windows, while the container-recommend extra verifies quay.io/biocontainers images for custom tool definitions.
What it helps with
- Trigger Galaxy analysis jobs and monitor job progress through chat
- Import and execute pipelines from the Intergalactic Workflow Commission
- Upload biological sequence files to histories and retrieve generated outputs
- Draft Galaxy markdown pages with embedded datasets and revisions
Example prompts for the agent
- Inspect the input parameters for the fastqc tool in my Galaxy instance
- Import the latest RNA-seq workflow from IWC and display its steps
- Create a new history and upload my sequence file from this local path
How to install galaxy-mcp
Platform CLI
claude mcp add galaxy-mcp -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcpReplace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>
Platform CLI
codex mcp add galaxy-mcp --env GALAXY_URL=<GALAXY_URL> --env GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcpReplace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>
Config file
{
"mcpServers": {
"galaxy-mcp": {
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>
Config file
{
"servers": {
"galaxy-mcp": {
"type": "stdio",
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}Replace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>
Platform CLI
gemini mcp add -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> galaxy-mcp uvx galaxy-mcpReplace <…> with your own values. uvx runs the command named after the package; if the README names another one, use uvx --from galaxy-mcp <command>
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about galaxy-mcp
How to install galaxy-mcp in Claude Code?
Run claude mcp add galaxy-mcp -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcp in your terminal. Replace the placeholders with your actual Galaxy instance address and personal access token.
What does galaxy-mcp do?
It enables coding assistants to interact with Galaxy servers, schedule computational tools, monitor histories, and orchestrate bioinformatics pipelines.
What does the container-recommend extra provide?
It resolves verified container images on quay.io/biocontainers for specified conda packages. This prevents runtime failures caused by fabricated image tags during custom tool creation.
