BD2KGenomics/cgl-docker-lib

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Python
Created over 9 years ago
Updated over 5 years ago

BD2KGenomics/cgl-docker-lib

BD2KGenomics

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toil-rnaseq

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

toil-scripts

Toil workflows for common genomic pipelines

protect

cgcloud

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

conductor

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

s3am

A fast, parallel, streaming multipart uploader for S3

hgvm-graph-bakeoff-evaluations

All code for reproducing reference graph bakeoff results

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

23andMe-brca-exchange

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

toil-lib

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

bd2k-python-lib

The BD2K Python module kitchen sink

brca-pipeline

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

dcc-metadata-indexer

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

core-operations

test repo for core operation

hgvm-builder

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

adam-contest-eval

Run ADAM variant calling against the 1000genomes.org dataset

vcf-to-ga

Generates GA4GH messages from VCF data

dockstore_tool_adtex

dcc-redwood-client

dockstore_workflow_fusion

Runs STARFusion and arriba

Common Workflow Language

10k-exomes

toil-rnaseq-sc

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

dockstore_workflow_snps

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

Common Workflow Language

dockstore_tool_varscan_cnv

Varscan copynumber variation caller workflow

toil-topmed

The repository for the Toil TOPMed alignment best practice workflow.

dcc-ops

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

hgvm

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

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.

dcc-metadata-schemas

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

dcc-redwood-compose

dockstore_tool_arriba

Implementation of structural variant finding algorithm arriba by Sebastian Uhrig

dcc-spinnaker

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

dcc-auth-proxy

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

parasol-binaries

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

dcc-action-service

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

dockstore-tool-gene-by-cell-creator

creates a gene by cell matrix from multiple slices

dcc-dockstore-tool-runner

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