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.