Setup and Installation¶
This guide deal with the general setup and local installation of the kallisto
program.
Contents
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.