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
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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