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@BD2KGenomics UC Santa Cruz Genomics Institute - Computational Genomics Lab

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    67 repositories

    • bd2k-python-lib

      Public
      The BD2K Python module kitchen sink
      Python
      •5•4•3•1•Updated Apr 13, 2026Apr 13, 2026

    • dcc-ops

      Public
      The UCSC Genomics Institute's Computational Genomics Platform (CGP). This repo contains the Docker compose-based deployment process.
      Shell
      •
      Apache License 2.0
      •4•2•51•2•Updated Dec 8, 2022Dec 8, 2022

    • dcc-dockstore-tool-runner

      Public
      A Dockstore tool designed to perform file downloads from Redwood, run another Dockstore tool, and then upload to Redwood.
      Python
      •
      Apache License 2.0
      •2•1•5•6•Updated Jul 29, 2022Jul 29, 2022

    • protect

      Public
      Python
      •
      Apache License 2.0
      •13•30•33•5•Updated Oct 6, 2021Oct 6, 2021

    • toil-rnaseq

      Public
      UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
      Python
      •
      Apache License 2.0
      •10•41•11•1•Updated Aug 17, 2020Aug 17, 2020

    • cgcloud

      Public
      Image and VM management for Jenkins, Spark and Mesos clusters in EC2
      Python
      •
      Other
      •17•22•49•3•Updated Jul 24, 2020Jul 24, 2020

    • 23andMe-brca-exchange

      Public
      Get expert, curated information about your 23andMe results in the BRCA1 and 2 regions
      Python
      •
      Other
      •3•5•0•2•Updated Oct 14, 2019Oct 14, 2019

    • toil-scripts

      Public
      Toil workflows for common genomic pipelines
      Python
      •
      Apache License 2.0
      •18•33•48•6•Updated Oct 3, 2019Oct 3, 2019

    • cgl-docker-lib

      Public
      Python
      •20•21•35•1•Updated Jul 3, 2019Jul 3, 2019

    • dockstore_workflow_snps

      Public
      Workflow for variant callers MuSE, MuTect, SomaticSniper, and Pindel
      Common Workflow Language
      •1•2•0•0•Updated May 16, 2018May 16, 2018

    • hgvm

      Public
      Python
      •
      Other
      •5•2•5•0•Updated May 7, 2018May 7, 2018

    • hgvm-graph-bakeoff-evaluations

      Public
      All code for reproducing reference graph bakeoff results
      Python
      •
      Other
      •6•9•0•1•Updated May 7, 2018May 7, 2018

    • dcc-auth-proxy

      Public
      Proxy in front of dcc services ensuring the right people are passed through with the right privileges
      JavaScript
      •
      Apache License 2.0
      •2•1•1•0•Updated Apr 28, 2018Apr 28, 2018

    • toil-workflows

      Public archive
      Modern Toil Workflows
      Common Workflow Language
      •
      Apache License 2.0
      •1•2•0•0•Updated Apr 28, 2018Apr 28, 2018

    • dcc-redwood-client

      Public
      Shell
      •
      Apache License 2.0
      •1•2•14•0•Updated Apr 27, 2018Apr 27, 2018

    • topmed-workflows

      Public archive
      a place for topmed workflows
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •23•1•0•0•Updated Apr 23, 2018Apr 23, 2018

    • dcc-metadata-indexer

      Public
      Scripts and schemas for JSON documents used with the DCC storage system and for building Elasticsearch indexes
      Python
      •
      Apache License 2.0
      •3•4•17•0•Updated Mar 30, 2018Mar 30, 2018

    • dcc-action-service

      Public
      A place for our business logic written in Luigi that triggers workflow launches.
      Python
      •
      Apache License 2.0
      •3•1•11•1•Updated Mar 26, 2018Mar 26, 2018

    • container-host-bag

      Public
      This is a playbook that sets up a container host which can run workflows in containers
      Python
      •
      GNU General Public License v3.0
      •5•1•0•0•Updated Mar 16, 2018Mar 16, 2018

    • dockstore_workflow_fusion

      Public
      Runs STARFusion and arriba
      Common Workflow Language
      •1•2•0•0•Updated Mar 8, 2018Mar 8, 2018

    • dockstore_tool_arriba

      Public
      Implementation of structural variant finding algorithm arriba by Sebastian Uhrig
      Shell
      •2•1•0•0•Updated Mar 8, 2018Mar 8, 2018

    • dcc-spinnaker-client

      Public
      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
      •
      Apache License 2.0
      •4•1•14•1•Updated Mar 7, 2018Mar 7, 2018

    • dockstore_tool_adtex

      Public
      R
      •2•2•0•0•Updated Feb 26, 2018Feb 26, 2018

    • platform-administration

      Public archive
      Issues representing platform epics, user stories, tasks, etc. that are not specific to an existing component repository.
      1•1•0•0•Updated Feb 7, 2018Feb 7, 2018

    • toil-topmed

      Public
      The repository for the Toil TOPMed alignment best practice workflow.
      Python
      •
      Apache License 2.0
      •2•2•0•0•Updated Jan 18, 2018Jan 18, 2018

    • dcc-storage

      Public archive
      Cloud object-based storage system for ICGC data
      Java
      •
      Other
      •11•3•6•0•Updated Nov 16, 2017Nov 16, 2017

    • dockstore_workflow_cnv

      Public
      Runs ADTEx and Varscan copynumber on input exome bam files
      4•1•1•0•Updated Nov 14, 2017Nov 14, 2017

    • dockstore_tool_varscan_cnv

      Public
      Varscan copynumber variation caller workflow
      Shell
      •2•2•1•0•Updated Nov 14, 2017Nov 14, 2017

    • core-operations

      Public archive
      test repo for core operation
      Python
      •1•3•0•0•Updated Oct 18, 2017Oct 18, 2017

    • toil-lib

      Public
      A common library for functions and tools used in toil-based pipelines
      Python
      •
      Apache License 2.0
      •7•4•11•7•Updated Oct 16, 2017Oct 16, 2017
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