Update Bracken data manager

[gallardoalba]

FOR CONTRIBUTOR:

• [x] - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• [x] - License permits unrestricted use (educational + commercial)
• [ ] - This PR adds a new tool or tool collection
• [ ] - This PR updates an existing tool or tool collection
• [x] - This PR does something else (explain below)

I think that it fixes a problem related to the Bracken databases: history.

[gallardoalba]

I have tested it locally, but not sure how to include a new test in the data manager itself @dfornika.

[bgruening]

@dfornika can you maybe look at this?

[gallardoalba]

I'm not sure how to fix the test, perhaps you have an idea @EngyNasr? Also, in the description I included a history with reproduce the problem with the current version.

[gallardoalba]

Thanks a lot @blankenberg, I was struggling with it.

[blankenberg]

My pleasure @gallardoalba. Mind doing a test install to confirm that it is actually working?

[gallardoalba]

My pleasure @gallardoalba. Mind doing a test install to confirm that it is actually working?

Sure!

[gallardoalba]

My pleasure @gallardoalba. Mind doing a test install to confirm that it is actually working?

Hi @blankenberg, sorry for the delay. Unfortunately, it is still failing:

[bernt-matthias]

Can this be bumped to 2.7?

[bernt-matthias]

Is https://github.com/galaxyproject/tools-iuc/issues/4141 fixed here?

[gallardoalba]

Not, it is still not working.

[bernt-matthias]

What is the state here? Tests seem to pass?

[gallardoalba]

What is the state here? Tests seem to pass?

I'll check it again tomorrow, but last time I tested in my local instance and I found still some errors.

[bernt-matthias]

Old but gold? Is this PR still needed?

[gallardoalba]

It is still needed, but it still doesn't work.. I'll try to work on it in a few days.

[pimarin]

The bracken nomenclature is a problem into the datamanager. I experienced it to standardize a workflow. The problem; I use kraken2 and bracken which deal with closed database but bracken need the database with kmer information so 2 data managers. I can submit by a logical input the name of database in kraken2 to be used : k2_pluspf_16gb_20210517 because the script use :

    database_value = "_".join([
        now,
        "standard",
        "kmer-len", str(kraken2_args["kmer_len"]),
        "minimizer-len", str(kraken2_args["minimizer_len"]),
        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
        "load-factor", str(kraken2_args["load_factor"]),

But for bracken if you use the equivalent input provided by your galaxy web server the tool failed with an error of database name :

parameter 'kmer_distr': an invalid option ('2023-08-24T153645Z_standard_prebuilt_pluspf_16gb_2022-06-07') was selected (valid options: bf6177af-7f5b-4005-9bec-fc7c89c3cb1c,41c59a90-3759-486c-b865-bcffc966adde) Using default: '41c59a90-3759-486c-b865-bcffc966adde'.

Because bracken use the uuid of the file : database_value = str(uuid.uuid4()) as : 41c59a90-3759-486c-b865-bcffc966adde But this information is not available by a simple user if he wants to use a workflow from a public repository