Load eQTL Catalogue data to DuckDB

The eQTL Catalogue REST API provides access to molecular QTL summary statistics and study metadata from the eQTL Catalogue project. Everything needed to build a working eQTL Catalogue → DuckDB pipeline is on this page: the API's base URL, authentication, endpoints, pagination and incremental field — plus a prompt that hands the whole job to your coding agent.

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Build your eQTL Catalogue to DuckDB pipeline

Paste this prompt into Claude, Codex, or Cursor. The agent does the rest.

PromptCopy prompt
Run uvx dlthub-init@latest to build a pipeline from eQTL Catalogue to DuckDB and run it on dltHub

That scaffolds a dltHub workspace and installs the dltHub AI harness — the project rules, the secrets-management skill, and the dlt MCP server your agent needs to work safely. From there it reads the eQTL Catalogue API, proposes the endpoints to load, then writes, runs and validates the pipeline while you review rather than type. Credentials are inspected through MCP tools, so your agent never reads secrets.toml itself. How the LLM-native workflow works →

Prefer to write it yourself? Every fact the agent uses is below.

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eQTL Catalogue API at a glance

These values come from the eQTL Catalogue API reference — the authoritative source if anything here looks out of date.

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How do I authenticate with the eQTL Catalogue API?

The eQTL Catalogue API is a public service and does not require authentication for data access.

1. Get your credentials

The eQTL Catalogue REST API is a public service provided by EMBL-EBI. It does not require any API keys, tokens, or registration to access. You can send GET requests directly to the API endpoints without providing any authentication headers.

2. Add them to .dlt/secrets.toml

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[sources.eqtl_catalogue_source]
# Note: The eQTL Catalogue API is public and does not require authentication. # The following is a placeholder structure if your dlt pipeline expects a # configuration block for consistency with other connectors. [sources.eqtl_catalogue]
api_key = ""

dlt reads this file automatically at runtime. With the harness, the setup-secrets skill prompts you for the values and never handles the raw credential in chat. For production, see setting up credentials with dlt.

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What eQTL Catalogue data can I load into DuckDB?

These are the eQTL Catalogue endpoints dlt can load into DuckDB:

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How do I load only new eQTL Catalogue records?

eQTL Catalogue exposes start on eqtl/api/v3/studies, so dlt can request only the records that changed since the last run. Set it as the cursor_path and dlt tracks the high-water mark for you between runs.

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{"name": "studies", "endpoint": {
    "path": "eqtl/api/v3/studies",
    "incremental": {"cursor_path": "start", "initial_value": "2024-01-01T00:00:00Z"},
}}

On the first run dlt loads everything from initial_value; on every run after that it requests only what changed and appends with write_disposition="merge" if you set a primary key. See incremental loading.

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What does the generated eQTL Catalogue pipeline look like?

A standard dlt REST API pipeline — the same code you would write by hand, loading /eqtl/api/v3/studies and /eqtl/api/v3/datasets from the eQTL Catalogue API into DuckDB:

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import dlt
from dlt.sources.rest_api import RESTAPIConfig, rest_api_resources

@dlt.source
def eqtl_catalogue_source(api_key=dlt.secrets.value):
    config: RESTAPIConfig = {
        "client": {
            "base_url": "https://www.ebi.ac.uk/eqtl/api/",
            "auth": {"type": "api_key", "api_key": api_key, "name": "token"},
        },
        "resources": [
            {"name": "studies", "endpoint": {"path": "eqtl/api/v3/studies"}},
            {"name": "datasets", "endpoint": {"path": "eqtl/api/v3/datasets"}}
        ],
    }
    yield from rest_api_resources(config)


def load_eqtl_catalogue_to_duckdb() -> None:
    pipeline = dlt.pipeline(
        pipeline_name="eqtl_catalogue_pipeline",
        destination="duckdb",
        dataset_name="eqtl_catalogue_data",
    )
    load_info = pipeline.run(eqtl_catalogue_source())
    print(load_info)


if __name__ == "__main__":
    load_eqtl_catalogue_to_duckdb()

Run it with python eqtl_catalogue_pipeline.py. The agent iterates on this until it loads cleanly — you review and approve, rather than write it from scratch.

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How do I query eQTL Catalogue data in DuckDB?

dlt creates one table per resource. Query the loaded data with Python or SQL — or ask your agent to, through the MCP server's execute_sql_query tool.

Python (pandas DataFrame):

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import dlt

data = dlt.pipeline("eqtl_catalogue_pipeline").dataset()
df = data.studies.df()
print(df.head())

SQL:

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SELECT * FROM eqtl_catalogue_data.studies LIMIT 10;

See querying your data with dataset and exploring it in marimo notebooks.

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How do I deploy the eQTL Catalogue to DuckDB pipeline in production?

The pipeline runs locally, which is ideal for prototyping and one-off analysis. When you need it on a schedule, monitored on every load, and shared with your team, deploy the same dlt code on the dltHub platform — no infrastructure to maintain. The prompt above already ends with "run it on dltHub", so your agent can take it there directly.

• Deploy & schedule — run the pipeline as a managed job with automatic retries.
• Monitor — observable job queues, alerting, and load metrics for every run.
• Transform — promote raw eQTL Catalogue loads into governed, documented models.
• Visualize & share — explore data in notebooks and publish live dashboards instead of static screenshots.

Book a demo →

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What other destinations can I load eQTL Catalogue data to?

dlt loads into any of these — only the destination argument changes:

Set dlt.pipeline(destination="snowflake") and add credentials in .dlt/secrets.toml. On the dltHub platform the same pipeline runs against a managed Iceberg lakehouse. See the full destinations list.

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Next steps

• Ready for production? Book a demo of the dltHub platform →
• dlt LLM-native workflow docs
• REST API source reference
• Join the dlt community on Slack