A toolset for data pipelines in Genomics

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).