Setup and Installation

This guide deal with the general setup and local installation of the kallisto program.

Main dependencies

click 7.1.2 Composable command line interface toolkit
numpy 1.20.1 NumPy is the fundamental package for array computing with Python.
scipy 1.6.0 SciPy: Scientific Library for Python
└── numpy >=1.16.5

For a list of all dependencies have a look at the pyproject.toml file.

Scientific References for Main Dependencies (if available)

1. Array programming with NumPy

2. SciPy 1.0: fundamental algorithms for scientific computing in Python

Install from PyPI

The kallisto program is available on PyPI. The installation is straightforward using pip

> pip install kallisto

Install from Source

Requirements to installkallisto from sources:

• poetry
• pyenv or conda
• python >=3.7

First check that poetry is running correctly (v1.0.10 at the time of writing)

> poetry --version
Poetry version 1.0.10

Create a virtual environment (via pyenv or conda) and activate it. Afterwards, clone the kallisto project from GitHub and install it using poetry

> git clone [e-mail]:AstraZeneca/kallisto.git
> cd kallisto
> poetry install