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A toolkit for ETL curation for the tranSMART data warehouse.

Project description

====
tmtk
====

Master:

.. image:: https://travis-ci.org/thehyve/tmtk.svg?branch=master
:target: https://travis-ci.org/thehyve/tmtk

.. image:: https://codecov.io/gh/thehyve/tmtk/branch/master/graph/badge.svg
:target: https://codecov.io/gh/thehyve/tmtk

.. image:: https://readthedocs.org/projects/tmtk/badge/?version=latest
:target: http://tmtk.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status

Develop:

.. image:: https://travis-ci.org/thehyve/tmtk.svg?branch=develop
:target: https://travis-ci.org/thehyve/tmtk

.. image:: https://codecov.io/gh/thehyve/tmtk/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/thehyve/tmtk


Anaconda Cloud latest package:

.. image:: https://anaconda.org/conda-forge/tmtk/badges/version.svg
:target: https://anaconda.org/conda-forge/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
------------

Installing via Anaconda Cloud or Pypi package managers
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Anaconda:

.. code:: sh

$ conda install -c conda-forge tmtk

Pypi:

.. code:: sh

$ pip3 install tmtk

Installing manually
^^^^^^^^^^^^^^^^^^^

Initialize a virtualenv
~~~~~~~~~~~~~~~~~~~~~~~

.. code:: bash

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


For mac users it will most likely be

.. code:: bash

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

or do this using `virtualenvwrapper`_.


Installation from source
~~~~~~~~~~~~~~~~~~~~~~

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

.. code:: sh

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

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

.. code:: sh

$ 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

Optional dependencies:
- mygene>=3.0.0

Licence
-------

LGPL-3.0

.. _transmart-batch: https://github.com/thehyve/transmart-batch/
.. _virtualenvwrapper: https://virtualenvwrapper.readthedocs.io
.. _readthedocs: https://tmtk.readthedocs.io/en/latest/
.. _examples: examples

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