installing Greengenes2 in a minimal environment

[Propolis4651 (John Hasty)]

Aloha Daniel,
I would like to install greengrenes2 in the smallest possible qiime environment. What is the "Minimal environment" for greengenes2?

For example, RESCRIPt which works fine for me.

conda create -y -n rescript
conda activate rescript
conda install \
  -c conda-forge -c bioconda -c qiime2 -c https://packages.qiime2.org/qiime2/2023.5/tested/ -c defaults \
  qiime2 q2cli q2templates q2-types q2-longitudinal q2-feature-classifier 'q2-types-genomics>2023.2' \
  "pandas>=0.25.3" xmltodict ncbi-datasets-pylib
-------------------------------------------
pip install git+https://github.com/bokulich-lab/RESCRIPt.git

When I try using that environment for greengenes2 I get rhe following error.

Failed to build iow
ERROR: Could not build wheels for iow, which is required to install pyproject.toml-based projects

Thanks,
John

[wasade (Daniel McDonald)]

Hi @Propolis4651,

A standard QIIME 2 2022.11 or 2023.2 environment should be sufficient as the installation should resolve dependencies. What specific command was used to install the q2-greengenes2 plugin and would it be possible to provide the full error output?

Best,
Daniel

[Propolis4651 (John Hasty)]

Hey Daniel,
I was working inside a docker container with conda and bash trying to get greengrenes2 into qiime2-2023.2 environment and was getting some kind of iow errors. But all of that is ancient history now that I'm back on square one. Currently I'm trying to get a docker container to start with the qiime2 environment activated, the way it stands now the user must do two things before they can use your plugin. After the container downloads you must (docker run -ti python-app bash) or in the second case (docker run -ti first-version bash) and then (conda activate qiime2-2023.2) the environment. Here's the docker pull links: (docker pull propolis/qiime2-2023.2-greengenes2-rescript:python-app) this one only has your plugin but (docker pull propolis/qiime2-2023.2-greengenes2-rescript:first-version) has both q2-greengenes2 and rescript but in separate environments. I'll let you known when i get it working properly,
Later,
John