MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows
Setup
Choose your client, copy the config, then fill in any required environment variables.
claude mcp add galaxy --env GALAXY_URL='<GALAXY_URL>' --env GALAXY_API_KEY='<GALAXY_API_KEY>' -- uvx galaxy-mcp~/.codex/config.toml
[mcp_servers.galaxy]
command = "uvx"
args = ["galaxy-mcp"]
env = { GALAXY_URL = "<GALAXY_URL>", GALAXY_API_KEY = "<GALAXY_API_KEY>" }
# codex mcp add galaxy --env GALAXY_URL='<GALAXY_URL>' --env GALAXY_API_KEY='<GALAXY_API_KEY>' -- uvx galaxy-mcp~/.cursor/mcp.json
{
"mcpServers": {
"galaxy": {
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}.vscode/mcp.json
{
"servers": {
"galaxy": {
"type": "stdio",
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}~/.gemini/settings.json
{
"mcpServers": {
"galaxy": {
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}claude_desktop_config.json
{
"mcpServers": {
"galaxy": {
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}.trae/mcp.json
{
"mcpServers": {
"galaxy": {
"command": "uvx",
"args": [
"galaxy-mcp"
],
"env": {
"GALAXY_URL": "<GALAXY_URL>",
"GALAXY_API_KEY": "<GALAXY_API_KEY>"
}
}
}
}Environment variables
GALAXY_URLGALAXY_API_KEY
Replace the placeholders with your own credentials and keep them out of version control.