RESCRIPT install: "ModuleNotFoundError: No module named 'q2_types_genomics'"

Technical Support
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Hi @mkweber, hopefully we can get this sorted out for you.

I just installed RESCRIPt into one of my older qiime2-2023.2 environments, and was able to run QIIME 2 and RESCRIPt successfully.

Some of the error outputs are a bit confusing as they reference qiime2-amplicon-2023.9 but your commands reference qiime2-2023.2. :man_shrugging:

One thing I noticed in our README, is that we forgot to update the conda activate qiime2-2023.2 line. It should be conda activate qiime2-2023.5 for that specific example. That is, the "http ... tested" folder we point to, should match the version of QIIME 2 being used. So, your command should be:

conda activate qiime2-2023.2
conda create -y -n rescript
conda activate rescript
conda install \
  -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.2/tested/ -c defaults \
  qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier 'q2-types-genomics>2023.2' \
  "pandas>=0.25.3" xmltodict ncbi-datasets-pylib

pip install git+https://github.com/bokulich-lab/RESCRIPt.git

If you are going to run the latest version of QIIME 2 (qiime2-amplicon-2023.9) you'll have to use the commands outlined here.

We'll get that README updated! :+1:

I just checked to see if these links under "hard mode" are still valid. It appears they are and I've been able download all of the files with wget. Perhaps there is a connection or firewall issue? Others had connection issues to SILVA a few days ago, perhaps their servers were down when you attempted to access the files?

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