galaxyproject / galaxyproject/training-material

Collection of tools and databases required for GTN that cannot be synchronized easily between the main servers

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Description

* humann nucleotide and protein database: https://github.com/galaxyproject/usegalaxy-tools/issues/855 (missing on AU/ORG)
* kraken2 - 5 toturials, multiple DBs - should all be updated to 2024 versions on the servers and the tutorials
* blastn: https://training.galaxyproject.org/topics/assembly/tutorials/assembly-decontamination/tutorial.html
* DBs for https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html

* phyloseq IT (only in EU)

Will try to add to this list step by step. Still need to check versions of the DBs on the servers if they exist.

Contributor guide

Open the contributing guide

Research direction

Start with the linked usegalaxy-tools issue and the Kraken2, blastn, and pathogen-detection tutorial URLs in the issue. Inventory the listed tools and databases across the servers and tutorials, then define completion as documenting the required versions and resolving the synchronization or availability gaps.

Written by the indexing model from the issue text.

Assessment

Domain
documentation, infrastructure
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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