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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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Mamba installation Problem #544

Closed ChristophKnapp closed 2 years ago

ChristophKnapp commented 2 years ago

Hi, I'm just getting started with metagenome-atlas. When I try to install, it tells me that my version of biopython is not correct.

Problem: package metagenome-atlas-2.9.0-pyhdfd78af_0 requires biopython 1.74.*, but none of the providers can be installed

I'm at an debian machine where the current version of biopython is 1.79. I would rather avoid downgrading it. Is there any way I can solve this?

Thanks a lot

Christoph

jmtsuji commented 2 years ago

Hi @ChristophKnapp , I think that the biopython requirement has been dropped in the latest version of ATLAS, v2.11.0. You could try installing that version.

ChristophKnapp commented 2 years ago

Thanks @jmtsuji for the fast reply. I'm afraid the situation is unchanged.

Problem: package metagenome-atlas-2.11.0-pyhdfd78af_0 requires biopython 1.74.*, but none of the providers can be installed

Regards

Christoph

SilasK commented 2 years ago

I made a fix, but it din't passed in the bioconda repository: https://github.com/bioconda/bioconda-recipes/pull/36226 Once this is passed, you should be able to install atlas v 2.11 without the biopython

What you can do now is creating a new environment with atlas installed. or install atlas from github see the instructions in the docs.

ChristophKnapp commented 2 years ago

Thank you @SilasK, the Mamba installation worked.