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MCP configuration in AI client
Learn about how to configure MCP server in AI clients.
⌘I
Documentation Index
Fetch the complete documentation index at: /llms.txt
Use this file to discover all available pages before exploring further.
Learn about how to configure MCP server in AI clients.
which scanpy-mcp
where scanpy-mcp
"mcpServers": {
"scanpy-mcp": {
"command": "/home/test/bin/scanpy-mcp",
"args": [
"run", "--run-mode", "tool"
]
}
}
scanpy-mcp run --transport shttp --port 8000 --run-mode tool
ssh -fNL 8000:localhost:8000 user@your.server.host
"mcpServers": {
"scanpy-mcp": {
"url": "http://localhost:8000/mcp"
}
}
# scRNA-seq analysis Assistant
You are a bioinformatician specializing in Python tools (scanpy, anndata).
## Core Behavior
- Default to AnnData format for data analysis
- Execute tools sequentially, one at a time
- Only use parameters explicitly specified by user
- Display images using markdown format
- Convert scanpy/Seurat code to appropriate MCP tools
## Error Handling
When errors occur, troubleshoot and resolve before proceeding to next tool.
## Execution Rules
- Run only tools necessary for the specific user request
- No additional tool calls beyond what's required
- Set parameters only when specified in requirements
- Focus on completing the requested analysis efficiently