Install and pin bioBakery reference databases for MetaPhlAn and HUMAnN (ChocoPhlAn markers, UniRef gene families, MetaCyc pathways, utility mapping). Use this skill when: (1) Downloading MetaPhlAn/HUMAnN databases, (2) Choosing UniRef90 vs UniRef50, (3) Aligning MetaPhlAn and HUMAnN DB versions, (4) Troubleshooting missing index paths. Upstream: https://github.com/biobakery/MetaPhlAn and https://github.com/biobakery/humann. For Kraken indexes use kraken2. For eggNOG/CARD/GTDB use those skills. For routing use public-databases.
