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usegalaxy.* common tools
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Add humann nucleotide and protein database for GTA training #855

Closed paulzierep closed 3 days ago

paulzierep commented 1 week ago

For the GTA we would need the humann nucleotide and protein database on org. It can be installed using toolshed.g2.bx.psu.edu/repos/iuc/data_manager_humann_database_downloader/data_manager_humann_download/3.6.0+galaxy0 and installing with the options:

Type of database to download: Nucleotide database Build for nucleotide database: Full

and

Type of database to download: Protein database Build for protein database: Full UniRef90

If there is a smarter a CI/code based way to request a DM run on org please let me know.

natefoo commented 4 days ago

I just copy from EU, but I can't tell exactly which they are?:

chocophlan-DEMO-3.0.0-12052021  Demo ChocoPhlAn for HUManN      3.0.0   /data/db/data_managers/humann/data/nucleotide_database/chocophlan-DEMO-3.0.0-12052021
chocophlan-full-3.0.0-13052021  Full ChocoPhlAn for HUManN      3.0.0   /data/db/data_managers/humann/data/nucleotide_database/chocophlan-full-3.0.0-13052021
chocophlan-full-3.6.0-29032023  Full ChocoPhlAn for HUManN 2023 3.6.0   /data/db/data_managers/humann/data/nucleotide_database/chocophlan-full-3.6.0-29032023

uniref-uniref90_diamond-3.0.0-13052021  Full UniRef90 for HUManN        3.0.0   /data/db/data_managers/humann/data/protein_database/uniref-uniref90_diamond-3.0.0-13052021
utility_mapping-full-uniref90-tol-lca-3.0.0-13052021    Mapping (full) for LCA for UniRef90     3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-uniref90-tol-lca-3.0.0-13052021.bz2
utility_mapping-full-map_level4ec_uniref90-3.0.0-13052021       Mapping (full) for Level-4 enzyme commission (EC) categories from UniRef90      3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_level4ec_uniref90-3.0.0-13052021.gz
utility_mapping-full-map_go_uniref90-3.0.0-13052021     Mapping (full) for Gene Ontology (GO) from UniRef90     3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_go_uniref90-3.0.0-13052021.gz
utility_mapping-full-map_uniref90_name-3.0.0-13052021   Mapping (full) between UniRef90 ids and names   3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_uniref90_name-3.0.0-13052021.bz2
utility_mapping-full-map_uniref50_uniref90-3.0.0-13052021       Mapping (full) for UniRef50 from UniRef90       3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_uniref50_uniref90-3.0.0-13052021.gz
utility_mapping-full-map_pfam_uniref90-3.0.0-13052021   Mapping (full) for Pfam domains from UniRef90   3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_pfam_uniref90-3.0.0-13052021.gz
utility_mapping-full-map_level4ec_uniref50-3.0.0-13052021       Mapping (full) for Level-4 enzyme commission (EC) categories from UniRef90      3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_level4ec_uniref50-3.0.0-13052021.gz
utility_mapping-full-map_ko_uniref90-3.0.0-13052021     Mapping (full) for KEGG Orthogroups (KOs) from UniRef90 3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_ko_uniref90-3.0.0-13052021.gz
utility_mapping-full-map_eggnog_uniref90-3.0.0-13052021 Mapping (full) for EggNOG (including COGs) from UniRef90        3.0.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_eggnog_uniref90-3.0.0-13052021.gz
uniref-uniref90_ec_filtered_diamond-3.6.0-29032023      EC-filtered UniRef90 for HUManN 2023    3.6.0   /data/db/data_managers/humann/data/protein_database/uniref-uniref90_ec_filtered_diamond-3.6.0-29032023
uniref-uniref90_diamond-3.6.0-29032023  Full UniRef90 for HUManN 2023   3.6.0   /data/db/data_managers/humann/data/protein_database/uniref-uniref90_diamond-3.6.0-29032023
utility_mapping-full-uniref90-tol-lca-3.6.0-29032023.bz2        Mapping (full) for LCA for UniRef90 2023        3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-uniref90-tol-lca-3.6.0-29032023.bz2
utility_mapping-full-map_ko_uniref90-3.6.0-29032023.gz  Mapping (full) for KEGG Orthogroups (KOs) from UniRef90 2023    3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_ko_uniref90-3.6.0-29032023.gz
utility_mapping-full-map_go_uniref90-3.6.0-29032023.gz  Mapping (full) for Gene Ontology (GO) from UniRef90 2023        3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_go_uniref90-3.6.0-29032023.gz
utility_mapping-full-map_pfam_uniref90-3.6.0-29032023.gz        Mapping (full) for Pfam domains from UniRef90 2023      3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_pfam_uniref90-3.6.0-29032023.gz
utility_mapping-full-map_uniref50_uniref90-3.6.0-29032023.gz    Mapping (full) for UniRef50 from UniRef90 2023  3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_uniref50_uniref90-3.6.0-29032023.gz
utility_mapping-full-map_level4ec_uniref50-3.6.0-29032023.gz    Mapping (full) for Level-4 enzyme commission (EC) categories from UniRef90 2023 3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_level4ec_uniref50-3.6.0-29032023.gz
utility_mapping-full-map_uniref90_name-3.6.0-29032023.bz2       Mapping (full) between UniRef90 ids and names 2023      3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_uniref90_name-3.6.0-29032023.bz2
utility_mapping-full-map_level4ec_uniref90-3.6.0-29032023.gz    Mapping (full) for Level-4 enzyme commission (EC) categories from UniRef90 2023 3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_level4ec_uniref90-3.6.0-29032023.gz
utility_mapping-full-map_eggnog_uniref90-3.6.0-29032023.gz      Mapping (full) for EggNOG (including COGs) from UniRef90 2023   3.6.0   /data/db/data_managers/humann/data/utility_mapping/utility_mapping-full-map_eggnog_uniref90-3.6.0-29032023.gz
natefoo commented 4 days ago

Per @bgruening:

uniref-uniref90_diamond-3.6.0-29032023  Full UniRef90 for HUManN 2023   3.6.0   /data/db/data_managers/humann/data/protein_database/uniref-uniref90_diamond-3.6.0-29032023
chocophlan-full-3.6.0-29032023  Full ChocoPhlAn for HUManN 2023 3.6.0   /data/db/data_managers/humann/data/nucleotide_database/chocophlan-full-3.6.0-29032023
natefoo commented 3 days ago

These are now deployed on .org via CVMFS.