q2-shogun install issue

Hi all,

I am trying to set up a new environment with qiime2-2020.6 plus a bunch of plug-ins I mainly use in my scripts.

One of them is q2-shogun which I’d love to give a proper try, and for that I followed the instructions:

conda install -c bioconda bowtie2

pip install https://github.com/knights-lab/SHOGUN/archive/master.zip

pip install https://github.com/qiime2/q2-shogun/archive/master.zip

qiime dev refresh-cache

I had no error message until the ‘refresh-cache’, which died with:
‘ValueError: Duplicate semantic type (‘Bowtie2Index’) defined in plugins: ‘shogun’ and ‘types’’

The result is that, in that conda environment any qiime2 command would trigger the failing ‘dev refresh-cache’ command … :face_with_raised_eyebrow:

Any suggestion to fix this, or at east I though was worth to flag this up if the developer attention is needed :thinking:


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