openbiomcp 0.1.1
BioOpenMCP: Model Context Protocol tools and CLI for bioinformatics workflows.
Requires Python: >=3.8

# OpenBioMCP

OpenBioMCP is a Python package for running Model Context Protocol (MCP) tools, including FastQC integration and other bioinformatics utilities with comprehensive background execution and status checking capabilities.

## Installation

```bash
pip install openbiomcp
```

## MCP Configuration

After installation, you need to configure the MCP server in Claude Desktop:

### Step 1: Find the installation path

**Mac:**
```bash
which openbiomcp
```
Example output: `/opt/anaconda3/bin/openbiomcp`

**Windows:**
```cmd
where openbiomcp
```
Copy the path from the output.

### Step 2: Configure Claude Desktop

Add the following configuration to your Claude Desktop settings:

```json
{
  "mcpServers": {
    "BioOpenMCP": {
      "command": "<PATH>"
    }
  }
}
```

**Example for Mac:**
```json
{
  "mcpServers": {
    "BioOpenMCP": {
      "command": "/opt/anaconda3/bin/openbiomcp"
    }
  }
}
```

Replace `<PATH>` with the actual path from Step 1.

### Step 3: Restart Claude Desktop

After adding the configuration, restart Claude Desktop to load the MCP server.


## Features

- **Modular design** - Organized by feature/domain for scalability
- **Background execution** - Run long-running bioinformatics tools without blocking
- **Real-time status monitoring** - Check job progress and retrieve results
- **Job management** - Start, stop, and clean up background jobs
- **CLI entry point** - Command-line interface for easy access
- **MCP integration** - Expose tools through Model Context Protocol
- **Ready for PyPI distribution**

## Available Bioinformatics Tools

| Tool | Purpose | Trigger Prompt Examples |
|------|---------|------------------------|
| **FastQC** | Quality control analysis for FASTQ files | "Run FastQC on my sample.fastq file"<br>"Check the quality of my sequencing data"<br>"Generate a quality report for sample_R1.fastq" |
| **Cutadapt** | Adapter trimming for sequencing data | "Trim adapters from my FASTQ file"<br>"Remove adapter sequences using cutadapt"<br>"Clean my sequencing data with adapter trimming" |
| **Trim Galore** | Automated adapter and quality trimming | "Run Trim Galore on my FASTQ file"<br>"Quality trim my sequencing data"<br>"Automatically trim adapters and low quality bases" |
| **STAR Alignment** | RNA-seq alignment tool | "Align my FASTQ files to the genome using STAR"<br>"Run RNA-seq alignment with STAR"<br>"Map my reads to the reference genome" |
| **MultiQC** | Aggregate bioinformatics analysis results | "Generate a MultiQC report for my analysis"<br>"Summarize all my QC results"<br>"Create a comprehensive report of my bioinformatics analysis" |

### Tool Categories

#### Quality Control
- **FastQC**: Comprehensive quality control analysis
- **MultiQC**: Aggregate and visualize QC results

#### Data Processing
- **Cutadapt**: Precise adapter trimming
- **Trim Galore**: Automated quality and adapter trimming

#### Alignment
- **STAR**: High-performance RNA-seq alignment
- **Genome Indexing**: Build STAR genome indices

#### Background Execution
All tools support background execution with real-time monitoring:
- Start jobs in the background
- Check job status and progress
- Retrieve results when complete
- Stop or cancel running jobs
- Clean up completed jobs