Install TADLib

Requirements

TADLib is developed and tested on UNIX-like operating system, and following Python packages are required:

  • Python 3.5+

  • numpy

  • scipy

  • matplotlib

  • scikit-learn

  • cooler

  • pomegranate 0.10.0+

  • networkx 1.x (not compatible with networkx 2.0 yet)

Install Conda

We strongly recommend using the conda package manager.

Note

If you have the Anaconda Distribution installed, you already have it.

Choose an appropriate Miniconda installer for your system, then in your terminal window type the following and follow the prompts on the installer screens:

$ bash Miniconda3-latest-Linux-x86_64.sh

After that, update the environment variables to finish the Conda installation:

$ source ~/.bashrc

Install the Required Packages

First set up the channels to make all packages listed above accessible (note that the order is important to guarantee the correct priority):

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge

Then just type and execute the following command:

$ conda install setuptools numpy scipy matplotlib scikit-learn cooler pomegranate=0.10.0 networkx=1

Install TADLib

Finally, TADLib can be installed from PyPI by pip:

$ pip install TADLib

TADLib has been installed successfully if no exception occurs in the above process.