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The\nTranSMART curation toolkit (``tmtk``) can be used to edit and validate\nstudies prior to loading them with `transmart-batch`_.\n\nFor general documentation visit `readthedocs`_.\n\nInstallation\n------------\n\nInstalling via Anaconda Cloud or Pip package managers\n^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAnaconda:\n\n.. code:: sh\n\n    conda install -c conda-forge tmtk\n\nPip:\n\n.. code:: sh\n\n    pip install tmtk\n\nInstalling manually\n^^^^^^^^^^^^^^^^^^^\n\nInitialize a virtualenv\n~~~~~~~~~~~~~~~~~~~~~~~\n\n.. code:: bash\n\n    python3 -m venv env\n    source env/bin/activate\n\n\nInstallation from source\n~~~~~~~~~~~~~~~~~~~~~~~~\n\nTo install *tmtk* and all dependencies into your Python environment,\nand enable the Arborist Jupyter notebook extension, run:\n\n.. code:: sh\n\n    pip install -r requirements.txt\n    python setup.py install\n\nor if you want to run the tool from code in development mode:\n\n.. code:: sh\n\n    pip install -r requirements.txt\n    python setup.py develop\n    jupyter-nbextension install --py tmtk.arborist\n    jupyter-serverextension enable tmtk.arborist\n\n\nRequirements\n^^^^^^^^^^^^\n\nThe dependencies are in ``requirements.txt``,\noptional dependencies are in ``requirements-dev.txt``.\n\n\nLicence\n-------\n\nLGPL-3.0\n\n.. _transmart-batch: https://github.com/thehyve/transmart-batch/\n.. _virtualenvwrapper: https://virtualenvwrapper.readthedocs.io\n.. _readthedocs: https://tmtk.readthedocs.io/en/latest/\n.. _examples: examples\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthehyve%2Ftmtk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fthehyve%2Ftmtk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fthehyve%2Ftmtk/lists"}