Qiime2

Introduction

This is a large, self-contained bioinformatics environment confected to tackle in particular microbiome studies.

Microbiome studies, do in fact pose special challenges, so the effort to cretae such a bioinformatitcs environment is jsutfied, but it does come at a cost of a certain unwieldiness in the software environment.

How to use

Qiime2 is installed within miniconda3 and this module must be loaded first:

module load miniconda3

After this the conda environment called "qiime2-2017.12" must be activated, this is done via:

source activate qiime2-2017.12

What then happens is that "qiime2-2017.12" then appears in the user's prompt and this verfies that the qiime2 environment has been activated, whether properly or improperly, remains to be seen.

Cautionary note

because qiime2 is built inside miniconda3 (also known as conda) it belongs in its very own environment that does not play ball very well with the cluster general software environment. While this doesn't prevent qiime2 not miniconda (conda) from running correctly, it does cause problems when leaving the qiime2/miniconda environment and landing in the cluster's environment modules system again.

In fact, there are conflicts which usually amount to the terminal session being unusable for anything else, and so the user must logout and log back in again, if they want to do something different.