tmtk

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

Clone the repo

$ git clone https://github.com/thehyve/tmtk
$ cd tmtk

Initialize a virtualenv

$ pip install virtualenv
$ virtualenv -p /path/to/python3.x/installation env
$ source env/bin/activate

For mac users it will most likely be

$ pip install virtualenv
$ virtualenv -p python3 env
$ source env/bin/activate

or do this using virtualenvwrapper.

Installing

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

$   pip3 install tmtk

or..

$   pip3 install -r requirements.txt
$   python3 setup.py install

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

$   pip3 install -r requirements.txt
$   python3 setup.py develop
$   jupyter-nbextension install --py tmtk.arborist
$   jupyter-serverextension enable tmtk.arborist

Requirements

These dependencies will have to be installed:

• pandas>=0.19.2
• ipython>=5.3.0
• jupyter>=1.0.0
• jupyter-client>=5.0.0
• jupyter-core>=4.3.0
• jupyter-console>=5.1.0
• notebook>=4.2.0
• requests>=2.13.0
• tqdm>=4.11.0
• mygene>=3.0.0

Licence

GPLv3