git clone https://github.com/your-username/samtools_mcp.git
cd samtools_mcp

pip install uv
uv pip install -r requirements.txt

{
  "servers": {
    "samtools": {
      "type": "docker",
      "image": "nadhir/samtools-mcp:latest",
      "volumes": [
        {
          "source": "/path/to/your/data",
          "target": "/data"
        }
      ]
    }
  }
}

{
  "samtools_mcp": {
    "command": "uv",
    "args": ["run", "--with", "fastmcp", "fastmcp", "run", "/path/to/samtools_mcp.py"]
  }
}

from samtools_mcp import SamtoolsMCP

mcp = SamtoolsMCP()
result = mcp.view(input_file="/data/example.bam")

result = mcp.sort(input_file="/data/example.bam", output_file="/data/sorted.bam")

result = mcp.index(input_file="/data/sorted.bam")

result = mcp.view(
    input_file="/data/example.bam",
    region="chr1:1000-2000",
    flags_required="0x2",
    output_format="SAM"
)

result = mcp.sort(
    input_file="/data/example.bam",
    output_file="/data/namesorted.bam",
    sort_by_name=True
)

result = mcp.depth(
    input_files=["/data/sample1.bam", "/data/sample2.bam"],
    region="chr1:1-1000000"
)