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.
Its name is
not qiime2. To see the help file, type
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.
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.