I’d like to run PICRUST2 in R so I don’t need to run it from a terminal by myself. I’ve installed the PICRUST2 environment via conda the first time, but due to my stupidness, I installed it inside another environment! The second time I tried to install it, for some reason the same steps for conda environment did not work. Therefore I installed mamba and then an environemtn for PICRUST2.

However when I tried to activate my PICRUST2 environment via mamba by mamba activate picrust2, it complains that

Run 'mamba init' to be able to run mamba activate/deactivate and start a new shell session. Or use conda to activate/deactivate.

Therefore I added mamba init to the command but the complain persists as if the mamba initiated does not work for the next command. This must be something I do not understand about the shell that a command is run via system or system2 in R.

I looked up how to activate conda environment in R. This post is perticularly helpful.

Firstly I tried to activate my env in R, which was successful.

  # activate PICRUST2
  if ('picrust2' %in% conda_list()[[1]]){
    use_condaenv('picrust2', required = TRUE)
  }else{
    print('no picrust2 environment')
  }

However, when I tried to run picrust2_pipeline.py via system, R acted like I’ve never activated picrust2.

Someone else suggested indicating the python in the picrust2 env:

path2python <- '/home/user/mambaforge/envs/picrust2/bin/python'
use_python(path2python, required = TRUE)

This also did not work.

Then I tried to indicate the full path to picrust2_pipeline.py in the system call. This works until picrust2_pipeline.py needs further excutables from the picrust2 environment, including place_seq.py, epa-ng,gappa, hsp.py,metagenome_pipeline.py,pathway_pipeline.py (don’t ask why I know!) They are all in the same path as picrust2_pipeline.py and soft-linking them to one of my current paths worked (totally cheating). Specifically for picrust2, you need to install the castor package in R. Oh my, runing R inside python inside R!

Of course a more reasonable solution would be adding the path to picrust2 (/home/user/mambaforge/envs/picrust2/bin/) to the $PATH via:

export PATH=$PATH:/path-to-picrust2/bin

So, my current answer to the title of this article is, no, you cannot enter a conda environment in R console. However one realization I had was that you can activate your mamba environment via conda. So conda activate picrust2 also works.