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genotoul-bioinfo / Binette

A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
https://binette.readthedocs.io
MIT License
13 stars 1 forks source link

DIAMOND 2.0.4: "DIAMOND failed to generate output" #13

Open RolandWirth opened 1 month ago

RolandWirth commented 1 month ago

Dear Developers,

Binette seems to be a useful program. However, with newer versions of Conda and Python, DIAMOND 2.0.4 does not work. The program needs to be upgraded to version 2.1.8 or newer. See: https://github.com/chklovski/CheckM2/issues/100. Unfortunately, it is not possible to manually replace or upgrade DIAMOND in Binette, as all dependent programs are also deleted by the conda install --force-reinstall diamond=2.1.8 command. You may want to upgrade to a newer version of CheckM2 if it is released (which will include the newer DIAMOND).

conda version: 23.3.1 mamba version: 1.4.2 Python version: 3.8.19

JeanMainguy commented 1 month ago

Hi @RolandWirth,

Thanks for pointing out the dependency issue. Binette relies heavily on CheckM2, so we're tied to its dependencies. We'll keep an eye on CheckM2 and update Binette once they've fixed the problem.

Best