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