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genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
GNU Affero General Public License v3.0
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Use conda to solve environment instead of mamba #59

Closed sofstam closed 2 years ago

sofstam commented 2 years ago

There are many conflicts with the latest version installation of mamba using conda and this GHaction failed. https://github.com/genomic-medicine-sweden/gms-artic/actions/runs/2412168987

The purpose of the code changes are as follows:

I used conda to build the container instead of mamba.

This version is a:

sofstam commented 2 years ago

When I build the container with conda instead of mamba, I get no errors in the GHaction: https://github.com/genomic-medicine-sweden/gms-artic/actions/runs/2415634431

henningonsbring commented 2 years ago

Have you tested this on an hpc? On hasta we got a lot of conda related problems. Please test that you can at least install this on hasta stage before merge.

sofstam commented 2 years ago

I am closing this PR since the issue with mamba was solved by the developpers.