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).
I walked through the install guide for q2-aldex2 (https://library.qiime2.org/plugins/q2-aldex2/24/), and jotted down my notes. I used a fresh installation of QIIME 2 2020.11, nothing else installed in that env:
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