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10k-exomes

23andme-brca-exchange

Get expert, curated information about your 23andMe results in the BRCA1 and 2 regions

adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

adam-contest-eval

Run ADAM variant calling against the 1000genomes.org dataset

bd2k-python-lib

The BD2K Python module kitchen sink

bioapi-examples

Code examples for working with web based bioinformatics APIs

brca-pipeline

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange

brca-website-deprecated

This repo is deprecated! Please use https://github.com/BD2KGenomics/brca-exchange

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2

cgl-docker-lib

cgl-hr

A public wiki for open projects in the CGL lab

conductor

Efficient, distributed downloads of large files from S3 to HDFS using Spark.

container-host-bag

This is a playbook that sets up a container host which can run workflows in containers

core-operations

test repo for core operation

cwltool-docker-host-docker

Common Workflow Language reference implementation

dcc-action-service

A place for our business logic written in Luigi that triggers workflow launches.

dcc-auth-proxy

Proxy in front of dcc services ensuring the right people are passed through with the right privileges

dcc-dockstore-tool-runner

A Dockstore tool designed to perform file downloads from Redwood, run another Dockstore tool, and then upload to Redwood.

dcc-feature-requests

Add feature requests for the UCSC GI Computational Platform here

dcc-metadata-indexer

Scripts and schemas for JSON documents used with the DCC storage system and for building Elasticsearch indexes

dcc-metadata-schemas

Repository for our JSON schema's used to describe our common metadata model.

dcc-ops

The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.

dcc-parent

Common parent pom for module configuration reuse

dcc-portal

Data portal for exploring and accessing data https://dcc.icgc.org/

dcc-redwood-client

dcc-redwood-compose

dcc-spinnaker

The server web service and UI for interacting with the Spinnaker validation system.

dcc-spinnaker-client

The submission system client that uploads data/metadata to Redwood and indicates to the Spinnaker web service that a submission bundle is ready for validation.

dcc-storage

Cloud object-based storage system for ICGC data