CNAG-Biomedical-Informatics/pheno-ranker

Pheno-Ranker is a tool for comparing phenotypic data structured in JSON/YAML format, such as Beacon v2 Models or Phenopackets v2.

Language: Perl - Size: 39 MB - Last synced at: about 2 hours ago - Pushed at: about 3 hours ago - Stars: 6 - Forks: 1

stjude-rust-labs/tes

A crate for working with the Task Execution Service (TES) specification.

Language: Rust - Size: 74.2 KB - Last synced at: 1 day ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 2

DNAstack/dnastack-client

The command line interface and client library for DNAstack services and GA4GH-compatible service, implemented in Python

Language: Python - Size: 734 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

ga4gh/va-spec-python

GA4GH Variation Annotation Python Implementation

Language: Python - Size: 63.5 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 2

ga4gh/vrs-python

GA4GH Variation Representation Python Implementation

Language: Python - Size: 17.5 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 55 - Forks: 31

elixir-cloud-aai/proTES

Proxy service for injecting middleware into GA4GH TES requests

Language: Python - Size: 475 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 8 - Forks: 6

broadinstitute/cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

Language: Scala - Size: 47.3 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1,011 - Forks: 361

phenopackets/phenopacket-schema

Repository for the GA4GH phenopacket schema

Language: Java - Size: 1.45 MB - Last synced at: 7 days ago - Pushed at: 7 months ago - Stars: 85 - Forks: 31

AustralianBioCommons/human-omics-data-sharing-field-guide

Prototype for Human Genomics Data Sharing Field Guide Website

Language: TeX - Size: 10.6 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 2 - Forks: 4

ohsu-comp-bio/funnel

Funnel is a toolkit for distributed task execution via a simple, standard API.

Language: Go - Size: 58.5 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 124 - Forks: 35

ga4gh/cat-vrs-python

GA4GH Categorical Variation Representation Python Implementation

Language: Python - Size: 40 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 1 - Forks: 3

bento-platform/bento_service_registry

Microservice implementing the GA4GH Service Registry API for the Bento platform.

Language: Python - Size: 1.38 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

elixir-cloud-aai/TESK

GA4GH Task Execution Service Root Project + Deployment scripts on Kubernetes

Language: Python - Size: 91.2 MB - Last synced at: 10 days ago - Pushed at: 3 months ago - Stars: 41 - Forks: 30

elixir-cloud-aai/cwl-WES

Trigger CWL workflows via GA4GH WES and TES

Language: Python - Size: 537 KB - Last synced at: 2 days ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 19

elixir-cloud-aai/elixir-cloud-aai.github.io

Documentation for the ELIXIR::GA4GH Cloud

Language: HTML - Size: 904 KB - Last synced at: 20 days ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 2

elixir-cloud-aai/tesk-api

GA4GH TES API Service that translates tasks into Kubernetes Batch API calls

Language: Java - Size: 519 KB - Last synced at: 20 days ago - Pushed at: about 2 months ago - Stars: 7 - Forks: 18

ga4gh/workflow-execution-service-schemas

The WES API is a standard way to run and manage portable workflows.

Size: 4.42 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 83 - Forks: 39

ga4gh/tool-registry-service-schemas

APIs for discovering genomics tools, their metadata and their containers

Language: Shell - Size: 9.57 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 31 - Forks: 18

bento-platform/bento_wes

Workflow execution service (based on GA4GH WES schemas) for the Bento platform.

Language: Python - Size: 1.33 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

elixir-cloud-aai/proWES

Proxy service for injecting middleware into GA4GH WES requests

Language: Python - Size: 465 KB - Last synced at: 20 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 5

elixir-cloud-aai/tesk-core

Python code that is launched as images into the Kubernetes cluster by tesk-api.

Language: Python - Size: 552 KB - Last synced at: 20 days ago - Pushed at: 4 months ago - Stars: 2 - Forks: 13

progenetix/beaconplus-web Fork of progenetix/progenetix-web

Web frontend for the bycon implementation of the Beacon v2 API

Language: JavaScript - Size: 7.75 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

ohsu-comp-bio/awesome-tes

A curated list of awesome GA4GH TES projects and programs

Size: 9.47 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

ga4gh-beacon/ga4gh-beacon-legacy-website

Website of ELIXIR Beacon - A GA4GH Driver Project

Language: HTML - Size: 61.6 MB - Last synced at: 18 days ago - Pushed at: 5 months ago - Stars: 7 - Forks: 8

EGA-archive/crypt4gh

GA4GH cryptographic tools

Language: Python - Size: 1.71 MB - Last synced at: 9 days ago - Pushed at: 9 months ago - Stars: 18 - Forks: 12

monarch-initiative/phenopacket-store

Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.

Language: Jupyter Notebook - Size: 28.9 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 15 - Forks: 4

elixir-cloud-aai/web-components

GA4GH Web components are the reusable custom elements that can be utilized in your web apps & web pages independently irrespective of what framework/library you are using to build the frontend.

Language: TypeScript - Size: 2.28 MB - Last synced at: 20 days ago - Pushed at: 23 days ago - Stars: 6 - Forks: 8

ga4gh/refget-compliance-suite

Repository for the Google Summer of Code for the Reference Retrieval API

Language: Python - Size: 823 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 7 - Forks: 6

guigolab/rnaget-client

Demo client for the GA4GH rnaget API

Language: Go - Size: 111 KB - Last synced at: 10 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

neicnordic/crypt4gh

Crypt4GH standard implementation

Language: Go - Size: 534 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 6 - Forks: 4

phenopackets/phenopacket-tools

An app and library for building, conversion, and validation of GA4GH Phenopackets.

Language: Java - Size: 7.43 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 5

ga4gh/ga4gh-server 📦

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

Language: Python - Size: 10.1 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 97 - Forks: 93

ga4gh/benchmarking-tools

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

Language: HTML - Size: 623 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 181 - Forks: 46

ohsu-comp-bio/task-execution-schemas Fork of ga4gh/task-execution-schemas

Language: Protocol Buffer - Size: 35.2 KB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

ohsu-comp-bio/beacon-team Fork of ga4gh-beacon/specification

GA4GH Beacon team repo

Language: Java - Size: 780 KB - Last synced at: about 1 year ago - Pushed at: about 10 years ago - Stars: 0 - Forks: 0

andrewyatz/refget-server-python

An implementation of the Refget v2.0.0 standard using Python

Language: Python - Size: 629 KB - Last synced at: 12 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

CSCfi/beacon-python 📦

Python-based GA4GH Beacon API Server

Language: Python - Size: 6.76 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 4

CSCfi/beacon-network 📦

Beacon Network APIs

Language: Python - Size: 1.47 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 4

ga4gh-beacon/specification-v2 📦

GA4GH Beacon v2 specification.

Size: 85 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 5

GA4GH-DREAM/dockstore-tool-synapse-get Fork of Sage-Bionetworks/dockstore-tool-synapse-get

Dockerized Synapse Python client & CWL for Dockstore

Language: Shell - Size: 13.7 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 2

GA4GH-DREAM/dockstore-tool-helloworld-checker

Language: Python - Size: 7.81 KB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 1

GA4GH-DREAM/dockstore-tool-helloworld

Language: Shell - Size: 2.93 KB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 7

EGA-archive/crypt4gh-rust

Rust implementation for the Crypt4GH encryption format

Language: Rust - Size: 2.07 MB - Last synced at: 24 days ago - Pushed at: 9 months ago - Stars: 5 - Forks: 2

BD2KGenomics/bioapi-examples

Code examples for working with web based bioinformatics APIs

Language: Jupyter Notebook - Size: 2.12 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 9 - Forks: 9

CSCfi/oidc-client 📦

General Purpose OIDC Client (with added ELIXIR AAI integration as default)

Language: Python - Size: 162 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

CSCfi/elixir-rems-proxy 📦

ELIXIR API for REMS

Language: Python - Size: 1.87 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

CSCfi/beacon-openshift 📦

ELIXIR Beacon Network Prototype APIs and UI

Language: Python - Size: 1 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

pnrobinson/phenotools

Validation of phenopackets in C++

Language: C++ - Size: 1000 KB - Last synced at: 12 days ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

sujaypatil96/ga4gh-va-schema

Data model for variant annotation in the GA4GH consortium.

Language: Python - Size: 1.16 MB - Last synced at: 16 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

BioContainers/biocontainers-backend

Python backend for Biocontainers (Flask + MongoDB)

Language: Python - Size: 1.08 MB - Last synced at: 10 days ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

ga4gh-metadata/metadata-schemas 📦

Schema definitions for the Global Alliance for Genomics and Health non-sequence objects

Size: 111 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

dockstore/write_api_service 📦

Implementation of tool-registry-schema with experimental write API support

Language: Java - Size: 170 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

labbcb/docker-ga4gh-shiny 📦

Docker image for GA4GHshiny application server

Language: R - Size: 4.88 KB - Last synced at: 5 months ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

labbcb/docker-ga4gh-server 📦

Docker image for hosting GA4GH reference implementation server

Language: Python - Size: 4.88 KB - Last synced at: 5 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

ga4gh-beacon/specification 📦

GA4GH Beacon specification.

Size: 16.2 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 32 - Forks: 25

bento-platform/bento_variant_service 📦

Variant search and GA4GH Beacon microservice for the Bento platform.

Language: Python - Size: 389 KB - Last synced at: 2 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ga4gh/tool-registry-validator

Used to validate APIs that implement https://github.com/ga4gh/tool-registry-schemas

Language: Python - Size: 69.3 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 1

ndopj/tesp-api

An Open-source implementation of a task execution engine based on the TES standard distributing executions to services exposing Pulsar application.

Language: Python - Size: 74.2 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 2

GA4GH-Pedigree-Standard/pedigree

Repository for the family history/pedigree project

Size: 1 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 3

sujaypatil96/ga4gh-va

LinkML schema for GA4GH variant annotation

Language: Jinja - Size: 1.67 MB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1

ga4gh/cloud-interop-ui

Manage Cloud interoperability test plugins and schedules through web interface

Language: JavaScript - Size: 920 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

icgc-argo/workflow-gateway

WES workflow API

Language: Dockerfile - Size: 45.9 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ga4gh/refget-loader

Schedule the processing of ENA sequences and upload to S3 public dataset

Language: Python - Size: 3.45 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

labbcb/espresso-caller

Automated and reproducible tool for identifying genomic variants at scale ☕️

Language: wdl - Size: 176 KB - Last synced at: 15 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Barski-lab/ga4gh_challenge

Workflow for GA4GH/DREAM challenge (phase 2)

Language: Common Workflow Language - Size: 1.63 MB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 5

ga4gh/refget-cloud

AWS serverless implementation of the refget service

Language: Python - Size: 6.41 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

ga4gh/cloud-interop-testing

Interoperable execution of workflows using GA4GH APIs

Language: Python - Size: 1.29 MB - Last synced at: about 1 month ago - Pushed at: almost 4 years ago - Stars: 9 - Forks: 8

jb-adams/ga4gh-autodocs

Tool for automated builds of GA4GH Standards documentation pages

Language: HTML - Size: 2.28 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

EMBL-EBI-TSI/WesCli

Multi-WES CLI client

Language: Python - Size: 97.7 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 3

monarch-initiative/monarch-mme

Matchmaker Exchange for Monarch

Language: Scala - Size: 1.05 MB - Last synced at: 12 days ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

GA4GH-DREAM/dockstore-tool-synapse-submit

Language: Shell - Size: 23.4 KB - Last synced at: about 1 month ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 0