Installation Guide


Python Environment

It is highly recommended to prepare a Python environment with the Anaconda or Miniconda distribution and install Arboreto’s dependencies using the conda package manager.

  • NumPy
  • SciPy
  • scikit-learn
  • pandas
  • dask
  • distributed

This avoids complexities in ensuring that libraries like NumPy and SciPy link against an optimized implementation of linear algebra routines.

Install using pip

The arboreto package is available from PyPI (Python Package Index), a repository of software for the Python programming language.

Using pip, installing the arboreto package is straightforward:

$ pip install arboreto

Check out the installation:

$ pip show arboreto

Name: arboreto
Version: 0.1.5
Summary: Scalable gene regulatory network inference using tree-based ensemble regressors
Author: Thomas Moerman
License: BSD 3-Clause License
Location: /vsc-hard-mounts/leuven-data/software/biomed/Anaconda/5-Python-3.6/lib/python3.6/site-packages
Requires: scipy, scikit-learn, numpy, pandas, dask, distributed


You can use pip to install arboreto in an Anaconda environment.

Install from source

Installing Arboreto from source is possible using following steps:

  1. clone the Github repository using the git tool:
$ git clone
$ cd arboreto
  1. build Arboreto using the provided script:
$ ./
  1. install the freshly built Arboreto package using pip:
$ pip install dist/*