# 1000 Genomes Project Dataset MCP Server
Real time access to _**1000 Genomes Project dataset**_, hosted online in _[Dnaerys variant store](https://dnaerys.org/)_
Sequenced & aligned by _New York Genome Center_ (_GRCh38_). _3202 samples_: 2504 unrelated samples from phase
three panel + 698 samples from 602 family trios ([dataset details](https://www.internationalgenome.org/data-portal/data-collection/30x-grch38))
### Key Features
- _real-time_ access to _138 044 723_ unique variants and _~442 billion_ individual genotypes
- variant, sample and genotype selection based on coordinates, annotations, zygosity
- filtering by VEP (impact, biotype, feature type, variant class, consequences), ClinVar Clinical Significance (202502),
gnomADe + gnomADg 4.1, AlphaMissense Score & AlphaMissense Class annotations
- filtering by inheritance model (de novo, heterozygous dominant, homozygous recessive)
- returned variants annotated with _HGVSp_, _gnomADe + gnomADg_, _AlphaMissense score_ + cohort-wide statistics
## Online Service
Remote MCP service via _Streamable HTTP:_
- http://db.dnaerys.org:80/mcp
- https://db.dnaerys.org:443/mcp
## Architecture
Implemented as a Java EE service, accessing _KGP dataset_ via gRPC calls to public Dnaerys variant store service.
- provides MCP over _Streamable HTTP_, _HTTP/SSE_ and _STDIO_ transports
- service implementation is based on [Quarkus MCP Server framework](https://docs.quarkiverse.io/quarkus-mcp-server/dev/)
## Available Tools
MCP tools and parameters are [here](./src/main/java/org/dnaerys/mcp/OneKGPMCPServer.java)
## Installation
Project can be run locally with MCP over _stdio_ and/or _http_ transports
#### Option A - build & run locally
- build the project and package it as a single _über-jar_:
- jar is located in `target/onekgpd-mcp-runner.jar` and includes all dependencies
```shell script
./mvnw package -DskipTests -Dquarkus.package.jar.type=uber-jar
```
- run it locally with _dev profile_
- both _stdio_ and _http_ transports are enabled
- http transport is on quarkus [http.port](./src/main/resources/application.properties)
- project expects _JRE 21_ to be available at runtime
```shell script
java -Dquarkus.profile=dev -jar <full path>/onekgpd-mcp-runner.jar
```
#### Option B - build & run in docker
- in order to run in docker, _stdio_ transport needs to be disabled to prevent application from stopping itself
due to closed stdio in containers
- it's already configured in _prod profile_
- it's the default configuration overall
- build with _prod profile_
```shell script
docker build -f Dockerfile -t onekgpd-mcp .
```
- run as you prefer, e.g.
```shell script
docker run -p 9000:9000 --name onekgpd-mcp --rm onekgpd-mcp
```
#### Option C - pull from Docker Hub
- pull prebuilt image; _stdio_ transport disabled, _http_ transport on port 9000
```shell script
docker pull dnaerys/onekgpd-mcp:latest
```
- run
```shell script
docker run -p 9000:9000 --name onekgpd-mcp --rm onekgpd-mcp
```
---
#### Connecting with MCP clients
- to connect via _http_ transport, _remote or local_, simply direct the client to a destination,
_e.g._ `http://localhost:9000/mcp` or `https://db.dnaerys.org:443/mcp`
- to connect via _stdio_ transport, MCP client should start application with _dev profile_ and with a full path to the jar file
- e.g. add to _Claude_ config files (e.g. `claude_desktop_config.json`):
```json
{
"mcpServers": {
"OneKGPd": {
"command": "java",
"args": ["-Dquarkus.profile=dev", "-jar", "/full/path/onekgpd-mcp-runner.jar"]
}
}
}
```
#### Verification
> How many variants exist in 1000 Genome Project ?
## License
This project is licensed under the Apache License 2.0 - see the [LICENSE](./LICENSE) file for details.
