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genome-genie's Introduction

A toolset for data pipelines in Genomics

Build Status

Dependencies

  • numpy
  • pandas
  • dask
  • dask.distributed
  • jinja2
  • glom
  • pyarrow
  • pysam

Instructions

  • Clone the source code with git:

      $ git clone https://github.com/suvayu/genome-genie.git
    
  • Install dependencies: all dependencies are available on conda-forge or PyPI, except for glom. Which is available only on PyPI. If you are using conda, you may install like this:

      $ conda install --file requirements-conda.txt
      $ pip3 install [--user] glom
    

    If you are using pip, you may install like this:

      $ pip3 install [--user] -r requirements.txt
    
  • To update (if you have not made any local changes), simply run:

      $ git pull
    
  • Install Genome Genie

      $ cd genome-genie
      $ pip3 install [--user] . -e
    

    The -e will allow you to update Genome Genie easily (no need to install again).

genome-genie's People

Contributors

suvayu avatar

Watchers

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genome-genie's Issues

VCF to parquet conversion

  • Flexible enough to handle the wide variety of VCFs (from different variant callers)
  • Performant enough to handle large VCFs

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