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CALYPR Tool Ecosystem

The CALYPR platform provides a suite of powerful, open-source tools designed to handle every stage of the genomic data lifecycle—from ingestion and versioning to distributed analysis and graph-based discovery.

Git-DRS

The Version Control Layer.
Git-DRS is a specialized extension for Git that manages massive genomic datasets using the GA4GH Data Repository Service (DRS) standard. It allows researchers to track, version, and share petabyte-scale files as easily as code, replacing heavy binaries with lightweight pointer files that resolve to immutable cloud objects.

Funnel

The Compute Layer.
Funnel is a distributed task execution engine that implements the GA4GH Task Execution Service (TES) API. It provides a standardized way to run Docker-based analysis pipelines across diverse environments—including Kubernetes, AWS, and Google Cloud—ensuring that your workflows are portable and independent of the underlying infrastructure.

GRIP

The Discovery Layer.
GRIP (Graph Resource Integration Platform) is a high-performance graph database and query engine designed for complex biological data. It enables analysts to integrate heterogeneous datasets into a unified knowledge graph and perform sophisticated queries that reveal deep relational insights across multi-omic cohorts.

Forge

Project formatting Forge scans a data repository to build an integrated FHIR based graph of samples and all the files connected to the project. It is responsible for schema checking and database loading. You can use it client side to verify and debug your project and on the server side, it is used to load databases.

Data Client

A client command line interface for interfacing with the Calypr system.

Sifter

Data Transformation Sifter is a tool for rapid data extraction and transformation.

Quickstart: Common Workflows

This section covers the three most common tasks. Choose your path based on your workflow:

1. Create a Project

Project creation is currently admin-mediated. Contact your data coordinator at support@calypr.org to request a new project. You'll receive:

  • GitHub repository URL
  • Calypr project ID
  • DRS server credentials

2. Upload & Download Data

Use Git-DRS for version-controlled data workflows (recommended for research teams):

  • Track files with Git LFS — files are registered with DRS automatically on push
  • Full version history alongside your data
  • Collaborate via standard Git workflows

See Git-DRS Quickstart

Use Data Client for direct file transfers without Git:

  • Simple upload/download of individual files
  • Useful for bulk transfers or non-versioned data
  • Programmatic access via CLI

See Data Client Data Management

3. Manage Collaborators

Add or remove team members from your project:

# Add a collaborator with read access
data-client collaborator add [project_id] colleague@example.com

# Add a collaborator with write access
data-client collaborator add [project_id] colleague@example.com --write

# Remove a collaborator
data-client collaborator remove [project_id] colleague@example.com

See Add Users for detailed documentation.

Getting Started

If you are new to the platform, we recommend starting with the Quick Start Guide to install the necessary binaries and set up your first workspace.