Test database for metaphlan4

Given the large amount of memory required to run metaphlan4 (from the docs: “minimum of 15GB or memory is needed”), it would be helpful to have a smaller database for testing purposes. This could also be useful for metaphlan4 CI testing, which seems to only comprise help-doc testing (MetaPhlAn/pythonpackage.yml at master · biobakery/MetaPhlAn · GitHub) – possibly due to the high memory that would be required for CI tests using the full metaphlan4 database.

Hi @nick-youngblut
We are currently working on building a toy database for our tutorials, I will ping you when it is available

Hi @nick-youngblut
You can find the toy database here: Index of /biobakery4/metaphlan_databases/toy_databases
It contains only the SGBs that are profilable in the tutorials available on github:
metaphlan4 · biobakery/biobakery Wiki · GitHub
strainphlan4 · biobakery/biobakery Wiki · GitHub
StrainPhlAn 4 · biobakery/MetaPhlAn Wiki · GitHub

That would be great! Once the toy database is created, I could help update the GitHub action for CI testing, if you’d like the contribution.

The toy database will really help with cloud-based development (e.g., GitHub Codespaces) where the memory and disk space are rather limited.