A toolkit for ETL curation for the tranSMART data warehouse.
Project description
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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:
$ conda install -c conda-forge tmtk
Pypi:
$ pip3 install tmtk
Installing manually
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.
Installation from source
To install tmtk and all dependencies into your Python environment, and enable the Arborist Jupyter notebook extension, run:
$ 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>=0.22.0
ipython>=5.3.0
jupyter>=1.0.0
jupyter-client>=5.0.0
jupyter-core>=4.3.0
jupyter-console>=5.1.0
notebook>=4.4.1
requests>=2.13.0
tqdm>=4.11.0
xlrd>=1.0.0
click>=6.0
arrow>=0.10.0
- Optional dependencies:
mygene>=3.0.0
Licence
LGPL-3.0
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