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.

qiime2's executable

Its name is

qiime

not qiime2. To see the help file, type

qiime --help

which gives you

(qiime2-2017.12) [ramon@marvin bladir0]$ qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...

 QIIME 2 command-line interface (q2cli)
 --------------------------------------

 To get help with QIIME 2, visit https://qiime2.org.

 To enable tab completion in Bash, run the following command or add it to
 your .bashrc/.bash_profile:

     source tab-qiime

 To enable tab completion in ZSH, run the following commands or add them to
 your .zshrc:

     autoload bashcompinit && bashcompinit && source tab-qiime

Options:
 --version  Show the version and exit.
 --help     Show this message and exit.

Commands:
 info                Display information about current deployment.
 tools               Tools for working with QIIME 2 files.
 dev                 Utilities for developers and advanced users.
 alignment           Plugin for generating and manipulating alignments.
 composition         Plugin for compositional data analysis.
 cutadapt            Plugin for removing adapter sequences, primers, and other unwanted sequence from sequence data.
 dada2               Plugin for sequence quality control with DADA2.
 deblur              Plugin for sequence quality control with Deblur.
 demux               Plugin for demultiplexing & viewing sequence quality.
 diversity           Plugin for exploring community diversity.
 emperor             Plugin for ordination plotting with Emperor.
 feature-classifier  Plugin for taxonomic classification.
 feature-table       Plugin for working with sample by feature tables.
 gneiss              Plugin for building compositional models.
 longitudinal        Plugin for paired sample and time series analyses.
 metadata            Plugin for working with Metadata.
 phylogeny           Plugin for generating and manipulating phylogenies.
 quality-control     Plugin for quality control of feature and sequence data.
 quality-filter      Plugin for PHRED-based filtering and trimming.
 sample-classifier   Plugin for machine learning prediction of sample metadata.
 taxa                Plugin for working with feature taxonomy annotations.
 vsearch             Plugin for clustering and dereplicating with vsearch.

Exiting qiime2 =

It helps alot if the user purposefully exists the qiime2 environment with:

source deactivate qiime2-2017.12

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.