Is there a way to ONLY install the dependencies for a specific workflow? (e.g., DADA2 workflow)

I'd like to use the DADA2 functionality of QIIME2 in a slimmed down environment. Do you currently have a way to do custom installations of just the required dependencies for such a workflow?

conda create new-env
conda activate new-env
conda install -c -c bioconda -c condo-forge q2-dada2

If you want q2cli too just include that after dada2.

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Is q2cli the command line interface?

So I would need the following:

  • qiime tools
  • qiime demux
  • qiime dada2
  • qiime feature-classifier
  • qiime phylogeny
  • (And command line interface)

Would I just create a fresh conda environment with the most recent channel + bioconda:
-c 2023.5-tested -c bioconda

Then install all of those modules?

Hello @jolespin,

Yes q2cli is the command line interface.

You'll get qiime tools automatically if you install q2cli.


conda create -n new-env q2-dada2 q2cli (...) -c (...)

will work too.

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Ended up doing this:

mamba install -c -c bioconda q2-feature-classifier q2-phylogeny q2-dada2 q2-demux q2cl

Haven't tested it yet but the install ran without errors.