isabl-mcp 0.2.0

MCP server providing AI agents access to the Isabl genomics platform

Isabl MCP Server

MCP server providing AI agents access to the Isabl genomics platform.

11 tools for querying data, searching applications, aggregating results, and searching the built-in knowledge base (347 documents from Isabl's source code, documentation, and API specs).

Quick Start

# Run directly with uvx (no install needed)
uvx isabl-mcp

# Or install with pip
pip install isabl-mcp
isabl-mcp

Set your credentials:

export ISABL_API_URL="https://your-isabl-instance.com/api/v1/"
export ISABL_API_TOKEN="your-token-here"

Tools (11)

Data Access

Tool	Description
isabl_query	Query any API endpoint with Django-style filters
isabl_get_tree	Get individual -> samples -> experiments hierarchy
isabl_get_results	Get result files from an analysis
isabl_get_logs	Get execution logs (stdout, stderr, script)

Query output convention

For experiment/sample/individual queries, use a human-readable identifier by default:

• Prefer ["system_id"] for experiments
• Use ["identifier"] when system_id is not available
• Include pk only when explicitly requested

Example:

isabl_query(
    endpoint="experiments",
    filters={"projects": 102},
    output_fields=["system_id"]
)

For analysis summaries:

• If analysis is individual_level_analysis, show individual system_id (for example IID_H210514) instead of long targets/references experiment lists.
• If analysis is project_level_analysis, show project pk instead of long targets/references experiment lists.
• Build frontend links from ISABL_API_URL by removing /api/v1/ and adding query params (for example ?analysis=<pk>).
• Before displaying a table, include a one-line summary of what the table shows (scope, filters, and count when available).

Applications

Tool	Description
get_apps	Search apps and get details (detailed=True for full info)
get_app_template	Get boilerplate code for new apps

Aggregation

Tool	Description
merge_results	Combine results from multiple analyses
project_summary	Get project statistics

Knowledge Base

Tool	Description
search_knowledge	Search 347 docs by keyword
get_knowledge_tree	Browse the knowledge tree hierarchy
get_knowledge_doc	Get full content of a document

Configuration

Variable	Description	Default
ISABL_API_URL	Isabl API base URL	http://localhost:8000/api/v1/
ISABL_API_TOKEN	API authentication token	(none)
ISABL_VERIFY_SSL	Verify SSL certificates	true
ISABL_TIMEOUT	HTTP timeout in seconds	30

Development

uv sync --dev
uv run pytest
uv run isabl-mcp     # start server

License

MIT