Can there be an update on the Galaxy Australia, please?

[lyisrae1]

Hello there,

This is more of a simple query instead of asking a question about help. I have been using PICRUSt2 on Galaxy (absolutely wonderful program!!) and I noticed that it is really out of date (version 2.5.3). I requested for the program to be updated through Galaxy, but they said that they would need the wrapper to be updated in order for them to do that.

Do you guys update the wrapper, and if so, can you send an updated version to Galaxy Australia, please?

Thank you for reading,
lyisrae1

[jennaj]

Note to Galaxy user's about how tools are hosted at Galaxy servers (from jennaj at Galaxy Help)

The tools hosted in Galaxy have a layer added around the original underlying tool we call a tool wrapper. These can be written by the original authors or others! The IUC is our tool standards group. Community contributions are big part of wrapping tools!

How it works: First a tool wrapper is created (or updated) and is published to the Main ToolShed. Once ready, Galaxy servers can host the tool!

The IUC created the current tool wrapper for PICRUSt2 (based on picrust2 (Version 2.5.3))

• Main ToolShed repository
• Development repository
• Request to update to picrust2-2.6.3 -> Request: update picrust2 wrapper for picrust2-2.6.3 galaxyproject/tools-iuc#7677

[R-Wright-1]

Thanks so much for this update @jennaj! I hadn't had a chance to look into this yet and wasn't familiar with how Galaxy servers work.

Hopefully someone else will get to the tool wrapper first - I'm unlikely to get to it soon, but will look into it if I have a chance.

Thanks,
Robyn

[bernt-matthias]

Thanks for the nudge :) I'm on it.

Is there by any chance a test for the full pipeline using --custom_trait_tables_ref1/2 and maybe --marker_gene_table_ref1 I would like to cover this case in the Galaxy tests.

The tests in https://github.com/picrust/picrust2/blob/master/tests/test_workflow.py seem to cover the old workflow.

[R-Wright-1]

test_traits_arc.txt
test_traits_bac.txt

I haven't had a chance to add specific tests for this to PICRUSt2 yet, but I do have some test files and full output if they are helpful:

wget http://kronos.pharmacology.dal.ca/public_files/picrust/picrust2_tutorial_files/chemerin_16S_arc.tar.gz
wget http://kronos.pharmacology.dal.ca/public_files/picrust/picrust2_tutorial_files/picrust2-v2.6.3-chemerin-out.tar.gz

The files within chemerin_16S_arc.tar.gz can be used as input, and the full output from running picrust2_pipeline.py -s chemerin_16S_arc/seqs_arc.fna -i chemerin_16S_arc/table.biom -o picrust2_out_pipeline -p 12 --verbose is in picrust2-v2.6.3-chemerin-out.tar.gz.

As a test for the custom trait tables, I think the two attached should work for this (you also should be able to simply run this with any subset of the existing bacteria/archaea default files).

Robyn

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