thehyve / tmtk

tranSMART Arborist ETL toolkit

tmtk

Master:

Develop:

Anaconda Cloud latest package:

A toolkit for ETL curation for the tranSMART data warehouse. The TranSMART curation toolkit (tmtk) can be used to edit and validate studies prior to loading them with transmart-batch.

For general documentation visit readthedocs.

Installation

Installing via Anaconda Cloud or Pip package managers

Anaconda:

conda install -c conda-forge tmtk

Pip:

pip install tmtk

Installing manually

Initialize a virtualenv

python3 -m venv env
source env/bin/activate

Installation from source

To install tmtk and all dependencies into your Python environment, and enable the Arborist Jupyter notebook extension, run:

pip install -r requirements.txt
python setup.py install

or if you want to run the tool from code in development mode:

pip install -r requirements.txt
python setup.py develop
jupyter-nbextension install --py tmtk.arborist
jupyter-serverextension enable tmtk.arborist

Requirements

The dependencies are in requirements.txt, optional dependencies are in requirements-dev.txt.

Licence

LGPL-3.0