RESCRIPT says it installed, but I cannot use it

Community Plugin Support
8

Hi @laur34,

We're still refining some details now that we have multiple distributions for 2023.9.

After corresponding with a few other :qiime2: devs, there are two approaches for making use of RESCRIPt:

  1. You can install into your current version of QIIME 2, using these updated commands:
conda install -c conda-forge -c bioconda -c qiime2 \
-c https://packages.qiime2.org/qiime2/2023.9/shotgun/released/  \
-c defaults   xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib

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

qiime dev refresh-cache

qiime rescript --help

I just tried this myself and it seems to work fine on my end.

  1. If the above does not work for you, you can install the shotgun distribution, which already has RESCRIPt installed, and simply switch to that environment and run RESCRIPt from there. Then switch back to the amplicon distribution to carry out the rest of your work.

Let us know if this works.

-Cheers!

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