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Documentation Index

Fetch the complete documentation index at: https://docs.scmcphub.org/llms.txt

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Agent library

You can use MCP servers in any Agent library which support MCP. If you haven’t used any AI library before, you can try Agno(https://docs.agno.com/introduction) Here is an simple example how to build a agent using scanpy-mcp within Agno. 
import asyncio

from agno.agent import Agent
from agno.tools.mcp import MCPTools
from agno.models.openai.like import OpenAILike

model = OpenAILike(
        id="qwen-plus",
        api_key="sk-**",
        base_url="https://dashscope.aliyuncs.com/compatible-mode/v1",
        extra_query={"enable_thinking": False},
    )


async def run_agent(message: str) -> None:
    """Run the filesystem agent with the given message."""
    async with MCPTools(
            "scanpy-mcp run --run-mode tool", timeout_seconds=60,
    ) as mcp_tools:        
        agent = Agent(
            model= model, 
            tools=[mcp_tools],
            show_tool_calls=True,
            debug_mode=True,
            description="""
            You are a bioinformatician. You are good at Python bioinformatic tool like scanpy, anndata, pandas.
            Run tools one by one. 
             """,
              monitoring=True
        )
        await agent.aprint_response(message, stream=True)



if __name__ == "__main__":

    asyncio.run(
        run_agent(
            "read /data20T/dev/scmcphub/scanpy-mcp/tests/data/hg19; "
            "then filter cells which gene number < 500; filter genes which express < 3 cells;"
            "compute qc metrics,include mitochondrial and ribosomal genes, plot total counts, 线粒体百分比，gene number 的小提琴图, 质控图使用multiple_pannel,;"
            "normalize and Logarithmize the data;"
            "Identify highly-variable genes; Reduce the dimensionality， 绘制pca_variance_ratio;"
            "perform cell clustering,设置resolution=0.5， 添加key leiden.0.5, "
            "and draw UMAP and TSNE scatter plot, color by leiden.0.5, PTPRC, NKG7,KLRD1,GNLY,CST7,PRF1, 每行显示3个图;"
            )
        )