Qiime2 - Revision history

Rf at 18:29, 29 January 2018

2018-01-29T18:29:57Z

Rf at 18:27, 29 January 2018

2018-01-29T18:27:56Z

Rf at 18:24, 29 January 2018

2018-01-29T18:24:03Z

Rf at 18:16, 29 January 2018

2018-01-29T18:16:47Z

Rf: Created page with "= Introduction = This is a large, self-contained bioinformatics environment confected to tackle in particular microbiome studies. Microbiome studies, do in fact pose special..."

2018-01-29T18:16:37Z

Created page with "= Introduction = This is a large, self-contained bioinformatics environment confected to tackle in particular microbiome studies. Microbiome studies, do in fact pose special..."

New page

= 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 qimme2 environment has been activated, whether properly or improperly, remains to be seen.

@@ Line 75: / Line 75: @@
    taxa                Plugin for working with feature taxonomy annotations.
    vsearch             Plugin for clustering and dereplicating with vsearch.
 = Cautionary note =

← Older revision		Revision as of 18:27, 29 January 2018
Line 17:		Line 17:

	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.		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.

	= Cautionary note =		= Cautionary note =

← Older revision		Revision as of 18:24, 29 January 2018
Line 17:		Line 17:

	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.		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.

← Older revision		Revision as of 18:16, 29 January 2018
Line 16:		Line 16:
	source activate qiime2-2017.12		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 ~~qimme2~~ environment has been activated, whether properly or improperly, remains to be seen.	+	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.