{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_spwwubzq8gxq","handle":"gigwa-mcp","url":"https://wellknown.network/agents/gigwa-mcp","links":{"self":"https://wellknown.network/agents/gigwa-mcp/record.json","html":"https://wellknown.network/agents/gigwa-mcp","markdown":"https://wellknown.network/agents/gigwa-mcp/record.md","api":"https://wellknown.network/api/v1/agents/gigwa-mcp","status":"https://wellknown.network/api/v1/agents/gigwa-mcp/status","claim":"https://wellknown.network/agents/gigwa-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/gigwa-mcp/claim.json","badge":"https://wellknown.network/agents/gigwa-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/gigwa-mcp/history","tools":"https://wellknown.network/api/v1/agents/gigwa-mcp/tools"},"ard":{"identifier":"urn:air::server:gigwa-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"gigwa-mcp","summary":"MCP server for driving Gigwa installations: import genotype/metadata, run QC and diversity analyses.","description":"<p align=\"center\">\n  <img src=\"docs/img/logo.png\" alt=\"Gigwa MCP\" width=\"460\">\n</p>\n\n[![gigwa-mcp MCP server](https://glama.ai/mcp/servers/gkanogiannis/gigwa-mcp/badges/card.svg)](https://glama.ai/mcp/servers/gkanogiannis/gigwa-mcp)\n\n[![MCP Badge](https://lobehub.com/badge/mcp/gkanogiannis-gigwa-mcp)](https://lobehub.com/mcp/gkanogiannis-gigwa-mcp)\n\n# Gigwa MCP Server\n\nAn [MCP](https://modelcontextprotocol.io) server that drives a local or remote\n[Gigwa](https://github.com/SouthGreenPlatform/Gigwa2) installation over its REST API.\nIt lets an MCP client (Codex CLI / Claude Desktop / Claude Code) run the whole genotyping workflow\nin plain language: **connect → import genotype data & metadata → run QC and diversity\nanalyses → audit databases for import artifacts**. Built for genomic-resources teams and\ngenebanks, but works with any Gigwa instance.\n\n- **Import** DArTseq SNP/Silico xlsx reports (with correct 2-row genotype calling) or\n  plain VCF, plus per-individual metadata.\n- **Analyse** read-only: genotypes are pulled out of Gigwa and all statistics are\n  computed in Python (scikit-allel / numpy / scipy). Nothing is written back.\n- **Audit** an existing instance to find databases that were imported badly.\n- Every analysis returns a chat summary and writes full tables as CSV under\n  `./gigwa_results/<database>/`.\n\n## Table of contents\n\n- [Gigwa MCP Server](#gigwa-mcp-server)\n  - [Table of contents](#table-of-contents)\n  - [Overview](#overview)\n  - [Features](#features)\n  - [How it works](#how-it-works)\n  - [Requirements](#requirements)\n  - [Installation](#installation)\n    - [Try it first (no install)](#try-it-first-no-install)\n    - [1. Get it](#1-get-it)\n    - [2. Point your client at it](#2-point-your-client-at-it)\n    - [Installing from the MCPB bundle](#installing-from-the-mcpb-bundle)\n  - [Run with Docker](#run-with-docker)\n  - [Configuration](#configuration)\n  - [Quick start](#quick-start)\n  - [Tool reference](#tool-reference)\n  - [Prompts \\& resources](#promp…","publisher":null,"homepage":null,"repository":null,"version":"1.9.2","license":null,"protocols":["mcp"],"tags":["mcp"],"pricing":null,"endpoints":[{"url":"pypi:gigwa-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","summary":"pypi","version":"pypi","description":"pypi"}},"derived":{"capabilities":[{"slug":"dev.docs-lookup","name":"Documentation Lookup","confidence":0.791,"provenance":"derived"},{"slug":"communication.chat","name":"Team Chat","confidence":0.745,"provenance":"derived"},{"slug":"documents.spreadsheets","name":"Spreadsheets","confidence":0.722,"provenance":"derived"}],"categories":["communication","dev","documents"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"gigwa-mcp","registry":"pypi","observedAt":"2026-10-28T01:26:51.206Z","publishedAt":"2026-09-12T16:15:31.729247Z","latestVersion":"1.9.2"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"gigwa-mcp","url":"https://pypi.org/project/gigwa-mcp/","firstSeenAt":"2026-09-09T16:23:51.749Z","fetchedAt":"2026-10-28T01:26:14.342Z","normalizedAt":"2026-10-28T01:26:14.342Z"}]},"firstSeenAt":"2026-09-09T16:23:51.749Z","updatedAt":"2026-10-28T01:26:51.206Z"}