Installation

Tejaas Installation Guide

If you encounter a problem during the installation procedure, please see the Troubleshooting Installation section in the FAQ for a possible solution.

Quick start

Tejaas is distributed via pypi. The simplest way to install a Python module from pypi is with pip:

pip install tejaas

but the work environment requires installing several components as discussed below.

Overview of Tejaas dependencies

To install Tejaas, you will need to have the following software on your computer:

1. Python (version 3.6 or greater).
2. Intel MKL library
3. any flavor of MPI linked to the Intel MKL library (e.g. OpenMPI)
4. Several Python modules, namely

• NumPy / array operations
• SciPy / optimization and other special functions
• statsmodel / used for ECDF calculation in JPA-score
• Pygtrie / used for reading MAF file in RR-score / maf null
• mpi4py / linked to MPI and MKL for python parallelization
• scikit-learn / used for PCA decomposition in KNN correction

Installing Tejaas requires setting up your computing environment to ensure that these components can communicate with each other. We will explain how to do this in the steps below.

1. Install python >= 3.6

To use Tejaas, you must have Python version 3.6 or greater. There are several ways you can install Python >= 3.6.

Our recommendation: Install Python via a conda-based package manager such as Miniconda or Anaconda. If you are starting from scratch, we recommend Miniconda.

Other options: Tejaas will also work with standalone distributions of Python (e.g., downloaded from Python.org), and the instructions below should work regardless of how Python is installed on your computer.

2. Check your Python installation

Tejaas is distributed via pypi. The simplest way to install a Python module from pypi is with pip. All recent Python versions are by default bundled with pip. Before running pip, check that you are running the version bundled with Python >= 3.6:

python --version
pip --version

If the reported Python version is or greater than 3.6.0 and pip is reported to come from that version (eg. pip 9.0.1 from /path/to/python (python 3.6)), then you are ready for the next step.

Important: In the instructions below, we assume your Python 3.6+ executable is python, and your pip (python 3.6+) executable is pip. However, you might need to replace python with python3 and pip with pip3.

If you already have an old version of Miniconda or Anaconda installed, but you do not have Python >= 3.6, see here for advice on how to proceed.