Setup and Installation

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

Getting the Program

kallisto runs on python3

Setup virtual environment

Python development setup. Install the pyenv python version manager:

> curl https://pyenv.run | bash

and add this to the ~/.bashrc and source it:

> export PATH="~/.pyenv/bin:$PATH"
> eval "$(pyenv init -)"
> eval "$(pyenv virtualenv-init -)"

Install the latest python versions

> pyenv install 3.8.2
> pyenv install 3.7.7
> pyenv local 3.8.2 3.7.7

You could also take conda to build a new virtual environment,

> conda create --name kallisto python=3.8

however, problems could occur while running the test suite due to some incompatibilities between poetry and conda, which may at the time of reading already been solved.

Install kallisto

Clone the repository

> git clone git@github.com:f3rmion/kallisto.git

Install a python package manager, where we choose to go with poetry

> curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
> source ~/.poetry/env

or alternatively via pip

> pip install --user poetry

Now, if you haven’t already done so, change into the cloned kallisto directory and download the dependencies via poetry:

> cd kallisto
> poetry install

Finally install the test automation environment nox via pip`

> pip install --user --upgrade nox

Run nox to test the setup (this may fail when you are using conda).

Getting Help from kallisto

Beside this manual you can check the in-program help by

> kallisto --help

The Verbose Mode

If you think some information is missing in your calculation you can switch to the verbose mode by using --verbose in the command line arguments.