UC Santa Cruz Genomics Institute - Computational Genomics Lab

bioapi-examples

Code examples for working with web based bioinformatics APIs

brca-website-deprecated

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

cgcloud

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

cgl-docker-lib

conductor

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

hgvm-graph-bakeoff-evaluations

All code for reproducing reference graph bakeoff results

protect

s3am

A fast, parallel, streaming multipart uploader for S3

toil-rnaseq

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

toil-scripts

Toil workflows for common genomic pipelines

BD2KGenomics/toil-rnaseq

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

BD2KGenomics/toil-scripts

Toil workflows for common genomic pipelines

BD2KGenomics/protect

BD2KGenomics/cgcloud

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

BD2KGenomics/cgl-docker-lib

BD2KGenomics/hgvm-graph-bakeoff-evaluations

All code for reproducing reference graph bakeoff results

BD2KGenomics/23andMe-brca-exchange

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

BD2KGenomics/bd2k-python-lib

The BD2K Python module kitchen sink

BD2KGenomics/dcc-metadata-indexer

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

BD2KGenomics/toil-lib

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

BD2KGenomics/core-operations

test repo for core operation

BD2KGenomics/dcc-storage

Cloud object-based storage system for ICGC data

BD2KGenomics/dcc-ops

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

BD2KGenomics/dcc-redwood-client

BD2KGenomics/dockstore_tool_adtex

BD2KGenomics/dockstore_tool_varscan_cnv

Varscan copynumber variation caller workflow

BD2KGenomics/dockstore_workflow_fusion

Runs STARFusion and arriba

BD2KGenomics/dockstore_workflow_snps

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

BD2KGenomics/hgvm

BD2KGenomics/toil-topmed

The repository for the Toil TOPMed alignment best practice workflow.

BD2KGenomics/toil-workflows

Modern Toil Workflows

BD2KGenomics/container-host-bag

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

BD2KGenomics/dcc-action-service

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

BD2KGenomics/dcc-auth-proxy

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

BD2KGenomics/dcc-dockstore-tool-runner

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

BD2KGenomics/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.

BD2KGenomics/dockstore_tool_arriba

Implementation of structural variant finding algorithm arriba by Sebastian Uhrig

BD2KGenomics/dockstore_workflow_cnv

Runs ADTEx and Varscan copynumber on input exome bam files

BD2KGenomics/platform-administration

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

BD2KGenomics/topmed-workflows

a place for topmed workflows