–version Show the version and exit.
–help Show this message and exit.
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.
fragment-insertion Plugin for extending phylogenies.
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
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.
Do you need to re-start the terminal or the environment after installation?
I have installed aldex2: conda install -c dgiguere q2-aldex2
then the command is still not found…qiime aldex2 --help
Right. But, you need the ALDEX2 library inside the qiime 2 enviroment. Each qiime2 environment (conda, docker, whatever) contains a separate R environment that can’t see other R packages outside of it. So, you need to follow the instructions above where you activate your qiime 2 environment, enter R via the command line, and check the installation there.
Thanks, keeps being frustrating, I have followed yours steps above. Seems like ALDEx2 is not being installed properly as it give me a lot of errors. So I believe there is an error whithin the system, where ALDEx2 is being installed but not under the qiime environment as a plugin. As this might be an issue specific to qiime, do you know any other forums I can get help with?
Hi @ecg - you shouldn’t have to mess around with any of the system-installed frameworks (in fact, I would strongly suggest leaving them alone, breaking those can have catastrophic results on other aspects of your system).
conda activate qiime2-2020.11
R -e 'install.packages("BiocManager", repos="http://cran.us.r-project.org")'
R -e 'BiocManager::install("ALDEx2")'
conda install -c dgiguere q2-aldex2 -y
qiime dev refresh-cache
qiime aldex2 --help
The last command printed out:
Usage: qiime aldex2 [OPTIONS] COMMAND [ARGS]...
Description: Analysis Of Differential Abundance Taking Sample Variation
Plugin website: https://github.com/ggloor/q2-aldex2
Getting user support: Please post to the QIIME 2 forum for help with this
--version Show the version and exit.
--citations Show citations and exit.
--help Show this message and exit.
aldex2 Analysis Of Differential Abundance
effect-plot Effect plots
extract-differences Extract differentially expressed features