Creating a Python environment for kaiju on aitken

Introduction

This file describes how to set up a python conda environment on aitken which can be used to run the kaiju code.

These steps assume that pip (only) is used for installing additional packages, and packages are only taken from PyPI.

These instructions assume you are using the bash shell.

Building the python environment

To create a Python environment for kaiju, we first install/load the Conda software package, then create the environment, then populate it with the required Python packages.

Note

These instructions are designed for novice users. If you are comfortable with building and managing conda-based environments, feel free to build your own environment using the NAS-provided conda software.

# Load the miniconda3 module.
module use -a /swbuild/analytix/tools/modulefiles
module load miniconda3/v4

# Now create the environment for kaiju, specifying only the python
# version.
conda create -n kaiju-3.12 python=3.12

# Activate the new environment.
conda activate kaiju-3.12

# Install the kaipy software.
# If you are using kaipy via pip:
pip install kaipy
# OR
# If you are using a clone of the kaipy repository:
cd /path/to/kaipy
pip install -e .
# -e is used to install the package in editable mode, which allows
# you to make changes to the code and have them reflected without needing
# to reinstall the package.

Using the python environment

Once your python environment is created, you must activate it for use with the kaiju software:

conda activate kaiju-3.12