Unable to install and use plug-ins

Community Plugin Support
1

Hi, I'm using a system provided installation of Conda (2022.10). I'm able to install QIIME 2 2023.2 successfully, but have been unable to install additional plugins from pip. I initially raised this on the q2-greengenes GitHub with @wasade, and a summary of what we tried so far is covered in #16. But I then realised its not just an issue with that plug in and the same thing happens when installing empress. Essentially, we can get pip to report a successful installation, however "qiime" does not appear to see the installed plugins. Would appreciate if you could help on this!

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Hello @elayt,

When you run qiime greengenes2 are you getting an "Error: QIIME 2 has no plugin/command named 'greengenes2'" message? Or is there some other issue?

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Hi colin, yes that is the error message.

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Hi @elayt,

Have you tried $qiime dev refresh-cache in your environment?

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Hi colin yes i tried still doesn’t show

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Hi @elayt,

I looked over the issue you shared above, and it seems like (as mentioned in the issue) this isn't an issue unique to q2-greengenes. I'm curious about the details of your machine and if it's possible for you to update your version of conda. Can you share what machine/OS you're using, and provide the results from running conda --version in your terminal?

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Hi @lizgehret

Actually I managed to resolve the issue now after a fair bit of troubleshooting with the help of my cluster administrators. The issue was that I did not have admin privileges to install packages in the central installation of anaconda v2022.10.

Some more info from the csf team:
The package needed to be installed in the environment 's libraries path ../.conda/envs/qiime2-2023.2 and not in the ~/.local/lib (this might cause conflicts with the default python version from CSF compared to the one in your conda environment). Please note that when you activate your environment with the installed packages there is no need to load again the anaconda module as it might cause conflicts with the libraries already installed in your environment. You can find the CSF OS details from executing "cat /etc/os-release" (CentOS Linux 7).

Hopefully this might help others if they face similar problems. We ended up doing an isolated pip install for the plug in to get around the issue. Thanks @wasade for your efforts on the GitHub issue!

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