Gemelli installation in q2-2026.4

[ARW-UBT]

Hello,
I moved on to the latest Qiime2 release (rachis-qiime2-2026.4) and realized that the workaround for q2-2025.4 is not that easy.
(in q2-amplicon-2025.4:
pip install Cython==0.29.37
pip install iow==1.0.7)

Do you have any advice how to install Gemelli in the q2-2026.4 release?
Would the rachis-tiny-2026.4 environment offer a solution for this issue?
I would like to continue using Gemelli :-)

Best regards

[cameronmartino]

Hi @ARW-UBT,

Thanks for letting me know. I made a fresh rachis-tiny-2026.4 env and was able to install gemelli with only

pip install gemelli

What error were you getting in the rachis-tiny-2026.4 trying to install gemelli?

[callaband]

I see that @cameronmartino responded while I was doing things. I also recently installed rachis-qiime2-2026 and it seemed to install without problem, but then I ran into errors. Here are the things I had to do to resolve errors:

/Users/user/miniforge3/envs/rachis-qiime2-2026.4/bin/pip install "setuptools>=80.9.0,<81.0.0" "tomlkit>=0.13.3,<0.14.0"

/Users/user/miniforge3/envs/rachis-qiime2-2026.4/bin/python -c "
util_path = '/Users/user/miniforge3/envs/rachis-qiime2-2026.4/lib/python3.12/site-packages/skbio/diversity/_util.py'
with open(util_path, 'a') as f:
f.write('\n_vectorize_counts_and_tree = vectorize_counts_and_tree\n')
print('Patch applied successfully!')
"
I haven't had any errors since and successfully used RPCA, did not use phyloRPCA yet.

[cameronmartino]

Ah, I see, thanks @callaband! Looks like I need to fix this for the newest version of skbio which removed _vectorize_counts_and_tree for vectorize_counts_and_tree. I will put in a PR soon. In the meantime, that is a good work around. Assuming the paths are the same, be sure to inspect those on your machine. :)

[ARW-UBT]

What error were you getting in the rachis-tiny-2026.4 trying to install gemelli?

Hi @cameronmartino , I got errors related to missing numpy and setuptools, but I do not have anymore the output from qiime dev refresh-cache.
I will try the q2-tiny env now.
Thanks a lot!

[ARW-UBT]

What error were you getting in the rachis-tiny-2026.4 trying to install gemelli?

Hi @cameronmartino
I just installed a fresh rachis-tiny-2026.4 and then pip install gemelli.
With qiime dev refresh-cache I get this message (only the first few lines, and replaced my username)

Traceback (most recent call last):
  File "/home/<USER>/miniconda3/envs/rachis-tiny-2026.4/lib/python3.12/site-packages/q2cli/util.py", line 277, in get_plugin_manager
    return qiime2.sdk.PluginManager.reuse_existing()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/<USER>/miniconda3/envs/rachis-tiny-2026.4/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 64, in reuse_existing
    raise UninitializedPluginManagerError
rachis.sdk.plugin_manager.UninitializedPluginManagerError

and the last line:
ModuleNotFoundError: No module named 'pkg_resources'

Best

[ARW-UBT]

Is there any suggestion how to handle the missing pck_ressources? There is this post on q2 forum stating that this module is slated fro removal. So, I am not installing it in the tiny environment for the moment.
Best

[cameronmartino]

Hi @ARW-UBT,

Thank you for letting me know. I put in a PR that will take a bit to review, merge, and be updated in pypi but for now you can use:

pip install git+https://github.com/biocore/gemelli.git@117-gemelli-installation-in-q2-20264

That is passing all tests now and should work in anything up to and including rachis-tiny-2026.4.

[ARW-UBT]

Hi @cameronmartino
Thank you for the workaround.
Installed it and had to add seaborn to overcome the q2 dev refresh-cache warning: ModuleNotFoundError: No module named 'seaborn'
Gemelli works in tiny as expected!
Great!

[cameronmartino]

@ARW-UBT , thanks for letting me know. Fixed!