Discover BD2KGenomics/dcc-metadata-indexer Open Source project

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Python
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Apache License 2.0
Created over 8 years ago
Updated over 6 years ago

BD2KGenomics

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

toil-rnaseq

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

Python

toil-scripts

Toil workflows for common genomic pipelines

Python

protect

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cgcloud

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

Python

cgl-docker-lib

Python

conductor

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

Scala

s3am

A fast, parallel, streaming multipart uploader for S3

Python

hgvm-graph-bakeoff-evaluations

All code for reproducing reference graph bakeoff results

Python

bioapi-examples

Code examples for working with web based bioinformatics APIs

Jupyter Notebook

brca-website-deprecated

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

JavaScript

23andMe-brca-exchange

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

Python

toil-lib

A common library for functions and tools used in toil-based pipelines

Python

bd2k-python-lib

The BD2K Python module kitchen sink

Python

brca-pipeline

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

Python

core-operations

test repo for core operation

Python

hgvm-builder

Tool to build a (Human) Genome Variation Map from a set of data sources

Python

adam-contest-eval

Run ADAM variant calling against the 1000genomes.org dataset

Shell

vcf-to-ga

Generates GA4GH messages from VCF data

Python

dockstore_tool_adtex

dcc-redwood-client

Shell

dockstore_workflow_fusion

Runs STARFusion and arriba

Common Workflow Language

10k-exomes

Python

toil-rnaseq-sc

Toil-based RNA-seq pipeline for processing single-cell data

Python

dockstore_workflow_snps

Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel

Common Workflow Language

dockstore_tool_varscan_cnv

Varscan copynumber variation caller workflow

Shell

toil-topmed

The repository for the Toil TOPMed alignment best practice workflow.

Python

dcc-ops

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

Shell

hgvm

Python

toil-workflows

Modern Toil Workflows

Common Workflow Language

ga4gh-gemini

Providing a GA4GH Interface to Gemini Variant Data

Protocol Buffer

hgvm-aligner-bakeoff-compliance

Tools and specifications for aligner behavior in the graph aligner bake-off

ga4gh-integration-deprecated

Tracking for ga4gh-integration projects

false-tandem-dup-finder

Scripts to find false tandem dups around scaffold gaps

Python

dockstore_workflow_cnv

Runs ADTEx and Varscan copynumber on input exome bam files

dcc-feature-requests

Add feature requests for the UCSC GI Computational Platform here

cgl-hr

A public wiki for open projects in the CGL lab

driver-projects

DREAMChallenges

a place to track work on the GA4GH Dream Challenges

platform-administration

Issues representing platform epics, user stories, tasks, etc. that are not specific to an existing component repository.

fhir-ga4gh-integration

Improve integration of FHIR Genomics and GA4GH

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.

Python

dcc-metadata-schemas

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

dcc-redwood-compose

Shell

dockstore_tool_arriba

Implementation of structural variant finding algorithm arriba by Sebastian Uhrig

Shell

dcc-spinnaker

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

Python

parasol-binaries

A stop-gap for hosting parasol binaries. If in doubt, ignore this.

dcc-auth-proxy

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

JavaScript

dcc-dockstore-tool-runner

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

Python

dcc-action-service

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

Python

dockstore-tool-gene-by-cell-creator

creates a gene by cell matrix from multiple slices

Python

BD2KGenomics/dcc-metadata-indexer

BD2KGenomics

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