Installation

Prerequisites

Python 3.11 or higher
pip or uv package manager
Git

Install from Source

git clone https://github.com/Hordago-Labs/biocontext7.git
cd biocontext7/packages/biocontext7
pip install -e ".[dev]"

Install with uv

git clone https://github.com/Hordago-Labs/biocontext7.git
cd biocontext7/packages/biocontext7
uv pip install -e ".[dev]"

Verify Installation

bc7 version

Expected output:

BioContext7 v0.1.0
Bioinformatics registry aggregator and pipeline generator

Optional Extras

BioContext7 supports optional dependency groups:

Extra	Description	Install
`dev`	Development tools (pytest, ruff, mypy)	`pip install -e ".[dev]"`
`api`	FastAPI REST server (uvicorn, redis)	`pip install -e ".[api]"`
`docs`	Documentation (MkDocs Material)	`pip install -e ".[docs]"`
`benchmarks`	Benchmarking tools (pandas, matplotlib)	`pip install -e ".[benchmarks]"`
`all`	Everything	`pip install -e ".[all]"`

MCP Server Setup

Claude Code (one-liner)

The fastest way to add BioContext7 to Claude Code:

# npx — auto-installs the package locally
claude mcp add biocontext7 -- npx -y @biocontext7/mcp@latest
 
# HTTP remote — zero install, connects to hosted API
claude mcp add --transport http biocontext7 https://mcp.biocontext7.com/mcp

See the Claude Code client guide for manual configuration and verification steps.

From source (Python)

For local development with the Python MCP server, add to ~/.claude/settings.json:

{
  "mcpServers": {
    "biocontext7": {
      "command": "python",
      "args": ["-m", "mcp_servers.biotools.server"],
      "cwd": "/path/to/biocontext7/packages/biocontext7"
    }
  }
}

CLI

Start the MCP server via the bc7 CLI:

bc7 serve                    # stdio transport (default)
bc7 serve --transport http   # HTTP transport on port 3000

Configuration

BioContext7 stores configuration in ~/.biocontext7/config.yaml.

# View current config
bc7 config show
 
# Set default pipeline target
bc7 config set default_target snakemake
 
# Set max search results
bc7 config set max_results 20

Default Settings

Setting	Default	Description
`default_target`	`nextflow`	Default compilation target
`prefer_nfcore`	`true`	Prefer nf-core modules when available
`max_results`	`10`	Maximum search results to display
`mcp_port`	`3000`	Port for HTTP MCP transport
`mcp_transport`	`stdio`	Default MCP transport (`stdio` or `http`)
`verbose`	`false`	Enable verbose output

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