Installation environment updated to Python 3.12

[ialbert]

We are now using a new version of BioConda built for Python 3.12

The automated install now uses that environment.

Post in this thread if you are seeing problems.

[njbowen]

so your best practice recommendation for existing users on previous versions would be to, just rerun the install script? or to update or create a new micromamba installation folder altogether? thanks.

[ialbert]

The problem is that conda and micromamba may not be the best neighbours; bash can get confused if both are active

My first choice would be to migrate from conda to micromamba. I would comment out the conda-specific bash initialization from .bashrc so that conda is not active by default.

then I would run the install script and get micromamba running and use that instead.

If one needs to use conda for some reason, then they can follow the instructions on the step-by-step page, but skipping the micromamba install step, and substituting micromamba with conda

[njbowen]

If already using micromamba but with an earlier version of python? Thanks.

[ialbert]

It should still work, one may not get the latest versions of samtools and such, perhaps,

but then micromamba is quicker at running tools from other environments

micromamba run -n OtherEnv  sometool

thus it is less of a problem.

[njbowen]

Right, just wondering if we should update to py3.12 to stay consistent with current course, etc.  thanks.

…

On Sep 17, 2025 at 3:10 PM -0400, Istvan Albert ***@***.***>, wrote: It should still work, one may not get the latest versions of samtools and such, perhaps, but then micromamba is quicker at running tools from other environments micromamba run -n OtherEnv sometool thus it is less of a problem. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[ialbert]

I usually recreate my entire environment every couple of years.

For example, when moving to micromamba, I deleted everything related to conda/mamba and then used micromamba. So, I don't have any information on how well the older instruction/environments work. The old environments should still work, but for new computers, I recommend using the latest instructions.

For people working in bioinformatics, the micromamba disruption is minor and almost negligible, maybe 30 minutes or so - after that, they have a much better version of conda that is free of the classic problem of conda (that of having a "base" environment).