Installation

The full python package can be installed using pip.

To make life easier, both the Python and other dependencies can be installed using conda.

First, ensure you have anaconda or miniconda installed.

Tip

I strongly recommend using mamba to install the dependencies. Mamba is essentially a compiled and parallelized version of conda. It will greatly speed up your installation.

After cloning this repo, please run:

cd arrakis/

conda env create
# or - if you have mamba:
mamba env create

This will install the python dependencies and the command-line scrips into a conda environment called spice, which can be activated by:

conda activate spice

An installation of Singularity is also required.

Attention

The version of Singularity that is required currently on conda-forge appears to be broken. For now, I will not include it in the conda environment. Please source it elsewhere for the time being.

That’s it!