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DennisSchmitz / Jovian_archive

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
GNU Affero General Public License v3.0
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Create helper environment via mamba #174

Open hexylena opened 3 years ago

hexylena commented 3 years ago

Hey y'all,

I was helping our two Avans students (Bob van Rijthoven, Diemo Perre) get Jovian setup and they'd been stuck on conda resolution. On a previous installation it'd gone very well, but, we needed to reconfigure and reinstall and it stuck for days at a time on creating the Jovian_helper_env. I didn't see anything obvious slowing down the resolution, but on running a manual conda env create -f ... with -vvv it was just stuck in the SAT solver.

Creating this environment via mamba was instantaneous in comparison. It seems you're using mamba already in some of the per tool environments, I think it may make sense for the helper environment (and the main env possibly?) to be created via mamba as well.

DennisSchmitz commented 3 years ago

Hi,

Thank you for your pull request! Yeah, this slipped through. Due to SARS2 our focus changed and we do not have the time to pick this up properly, which is also why I didn't reply promptly.

I'll leave this pull request open for now since the method you suggest causes problems due to nested environments on our work-environment. A similar solution as for the Jovian_master environment is required where first an empty env is created using conda which contains just the conda and mamba packages, then activate the conda env and update it via mamba as shown here: https://github.com/DennisSchmitz/Jovian/blob/77422ff0083309b24f6b2633112f1d03eb46c02a/bin/includes/Install_jovian-master#L27.

Again, thank you very much for bringing this to our attention! Although the changes are minimal the validation on our production setup will take some time, it will be picked up and included in the next (minor) version release so it can be validated in one go.

Kind regards, Dennis

hexylena commented 3 years ago

No worries @DennisSchmitz, completely understand the validation issue. No rush from us to merge, we'll just keep using this patch locally until you're all ready!