Hi all,
I am trying to work through the the CMI Tutorial, and run QIIME 2 via the proposed R commands.
However, I am unable to get past the first step. I've not been able to find any tutorials that explicitly discuss how this would work... So, here is what I've tried:
I activated my environment and then ran R:
(base)$ conda activate qiime2-amplicon-2025.4
(qiime2-amplicon-2025.4)$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(reticulate)
> Metadata <- import("qiime2")$Metadata
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'qiime2'
Run `reticulate::py_last_error()` for details.
What is the preferred way to run QIIME 2 via R? Are there other commands or packages I need to load, install, or fix?