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 https://packages.qiime2.org/qiime2/2023.5/tested/ -c bioconda -c condo-forge q2-dada2
If you want q2cli too just include that after dada2.
2 Likes
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.
Yes,
conda create -n new-env q2-dada2 q2cli (...) -c (...)
will work too.
1 Like
Ended up doing this:
mamba install -c https://packages.qiime2.org/qiime2/2023.7/tested/ -c bioconda q2-feature-classifier q2-phylogeny q2-dada2 q2-demux q2cl
Haven't tested it yet but the install ran without errors.
2 Likes