MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows
Connect Runs on your machine
claude mcp add galaxy-mcp -e GALAXY_URL=<GALAXY_URL> -e GALAXY_API_KEY=<GALAXY_API_KEY> -- uvx galaxy-mcp==1.3.0
{
"mcpServers": {
"galaxy-mcp": {
"command": "uvx",
"args": [
"galaxy-mcp==1.3.0"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}
{
"mcpServers": {
"galaxy-mcp": {
"command": "uvx",
"args": [
"galaxy-mcp==1.3.0"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}
{
"servers": {
"galaxy-mcp": {
"type": "stdio",
"command": "uvx",
"args": [
"galaxy-mcp==1.3.0"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}
Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.
Tools
This server runs locally, so its tools are listed by your MCP client once it starts.
Environment variables
| Name | Description |
|---|---|
GALAXY_URLRequired | URL of the Galaxy instance to connect to (e.g., https://usegalaxy.org) |
GALAXY_API_KEYRequired, secret | API key for authenticating with the Galaxy instance |
Details
| Package | [email protected] (PYPI, stdio) |
| First published | 29 Jan 2026 |
| Last updated | 29 Jan 2026 |
| Registry name | io.github.galaxyproject/galaxy-mcp |
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