@BD2KGenomics

UC Santa Cruz Genomics Institute - Computational Genomics Lab

Developers in the Computational Genomics Lab at the UC Santa Cruz Genomics Institute

  • Python 18 19 Updated Oct 17, 2018
  • UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

    Python 20 4 Apache-2.0 Updated Oct 1, 2018
  • The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.

    Shell 1 4 Apache-2.0 Updated Jun 25, 2018
  • Python 17 6 Apache-2.0 Updated Jun 5, 2018
  • Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel

    Common Workflow Language Updated May 16, 2018
  • Python 1 4 Updated May 7, 2018
  • All code for reproducing reference graph bakeoff results

    Python 8 4 Updated May 7, 2018
  • The BD2K Python module kitchen sink

    Python 3 5 Updated May 3, 2018
  • Proxy in front of dcc services ensuring the right people are passed through with the right privileges

    JavaScript 1 Apache-2.0 Updated Apr 28, 2018
  • toil-workflows Archived

    Modern Toil Workflows

    Common Workflow Language Apache-2.0 Updated Apr 28, 2018
  • Shell 1 Apache-2.0 Updated Apr 27, 2018
  • a place for topmed workflows

    wdl 10 BSD-3-Clause Updated Apr 23, 2018
  • Scripts and schemas for JSON documents used with the DCC storage system and for building Elasticsearch indexes

    Python 3 2 Apache-2.0 Updated Mar 30, 2018
  • A place for our business logic written in Luigi that triggers workflow launches.

    Python 2 Apache-2.0 Updated Mar 26, 2018
  • This is a playbook that sets up a container host which can run workflows in containers

    Python 4 GPL-3.0 Updated Mar 16, 2018
  • A Dockstore tool designed to perform file downloads from Redwood, run another Dockstore tool, and then upload to Redwood.

    Python Apache-2.0 Updated Mar 14, 2018
  • Runs STARFusion and arriba

    Common Workflow Language Updated Mar 8, 2018
  • Implementation of structural variant finding algorithm arriba by Sebastian Uhrig

    Shell Updated Mar 8, 2018
  • 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 3 Apache-2.0 Updated Mar 7, 2018
  • R 1 Updated Feb 26, 2018
  • Issues representing platform epics, user stories, tasks, etc. that are not specific to an existing component repository.

    Updated Feb 7, 2018
  • Image and VM management for Jenkins, Spark and Mesos clusters in EC2

    Python 21 18 Updated Feb 6, 2018
  • The repository for the Toil TOPMed alignment best practice workflow.

    Python 1 2 Apache-2.0 Updated Jan 18, 2018
  • Toil workflows for common genomic pipelines

    Python 26 17 Apache-2.0 Updated Jan 18, 2018
  • dcc-storage Archived

    Forked from overture-stack/score

    Cloud object-based storage system for ICGC data

    Java 2 6 GPL-3.0 Updated Nov 16, 2017
  • Runs ADTEx and Varscan copynumber on input exome bam files

    2 Updated Nov 14, 2017
  • Varscan copynumber variation caller workflow

    Shell Updated Nov 14, 2017
  • test repo for core operation

    Python 2 1 Updated Oct 18, 2017
  • A common library for functions and tools used in toil-based pipelines

    Python 2 7 Apache-2.0 Updated Oct 16, 2017
  • a place to track work on the GA4GH Dream Challenges

    Updated Sep 8, 2017
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