Discover DataBiosphere/encode-ingest Open Source project

Open-source command-line tool to run batch computing tasks and workflows on backend services such as Google Cloud.

896

dsub

Web user interface for the Terra platform

262

terra-ui

leonardo

terra-docker

job-manager

Job Manager API and UI for interacting with asynchronous batch jobs and workflows.

Common data model proposal for biomedical research intended to facilitate and encourage data sharing and reuse

terra-interoperability-model

terra-workspace-manager

The Terra Data Repository built by the Jade team.

jade-data-repo

a place for topmed workflows

topmed-workflows

terra-cli

data-browser

data-explorer

consent

data-portal

duos-ui

consent-ontology

Utilities for the Terra notebook environment.

terra-notebook-utils

Fast streams for block gzip files.

bgzip

Examples for use in data analysis.

terra-examples

Metadata indexer and query service used for AnVIL, HCA, LungMAP, and CGP

azul

Concurrent reads of HTTP URL addressed data

getm

terra-landing-zone-service

Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.

analysis_pipeline_WDL

WDL

hca-ingest

terra-app

Broad FHIR is a FHIR Server that powers applications for Genomics research.

FHIR

Synchronize Github issue and PR labels between two repositories

sync-github-labels

terra-cloud-resource-lib

Terra Resource Buffering Service

terra-resource-buffer

terra-external-credentials-manager

Example notebooks and documentation for working with the Terra Axon UI.

terra-axon-examples

terra-billing-profile-manager

terra-workspace-data-service

terra-java-project-template

Version control, test, and CI/CD your Python Jupyter notebooks.

herzog

UI for the Jade Data Repo

jade-data-repo-ui

data-explorer-indexers

Metrics collection service

bard

consent-data-use

welder

Batch ETL pipeline to mirror ClinVar releases into the Jade Data Repository.

clinvar-ingest

Lightly modified versions of htslib and bcftools to merge VCF streams.

xsamtools

terra-policy-service

AWS and GCP data storage system for genomic data.

data-store

calhoun

Notebook preview service

terra-azure-relay-listeners

consent-ui

A repo to track various TOPMed and other datasets

HTML

commons-sample-data

Data Biosphere GitHub Actions

github-actions

Terra UI automated prod deploy service

wdl-conformance-tests

WDL

topmed-workflow-variant-calling

WDL

saturn-ui-prod-deploy

cbas

biocore-data-model

tanagra

Repo for the Tanagra service being developed by the All of Us DRC

terra-aws-resource-discovery

firecloud-app

terra-drs-hub

Repository for the Terra "Axon" UI

terra-axon-ui

kernel-service-poc

featured-notebooks

Provides access to DSS azul-index in the Data Object Service schemas

dos-azul-lambda

rex

Survey response service

terra-gcs-bq-streaming-functions

Stairway saga transaction processor library

stairway

Janitor service to cleanup resources created by Cloud Resource Library (CRL)

terra-resource-janitor

Simple data storage system for AWS and GCP

ssds

example of maintaining authorization list via github + travis + s3

example-authz-registry

Bulk file-transfer system for data ingest

transporter

Amphibious new data transformer to prepare various sources for CGP DSS Data Loader

newt-transformer

Test user allocation service

lyle

JavaScript library for shared client-side analytics across DSP

bard-client

bond

Account linking service

Base framework environment k8s resources

env-base

hca-metadata-api

A library for processing HCA metadata programmatically

data-store authentication infra management

data-store-auth

java-pfb

terra-azure-arm-templates

Terraform definitions for all Saturn-managed repos and GCS projects

saturn-terraform

HCL

metadata-serialization

Serializing metadata for use and reuse ✒️📋🗃️💻

hamm

Cloud Cost Management Service

A package that provides the generated ANTLR4 WDL parsers for Python.

wdl-parsers

This supports integration testing between components for the biodata catalyst grant.

saturn-documentation

bdcat-integration-tests

terra-folder-manager

A utility to validate a staging area before it is imported.

hca-import-validation

terra-test-runner

terra-data-catalog

Components of the Commons Alliance

data-platforms

cbas-ui

findable-ui