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[24.1] Add bcsp datatype #19365

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merged 2 commits into from
Dec 28, 2024

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SantaMcCloud
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Hello,

this PR should add the new datatype bcsp. Sadly there is no docomuentation to it but it is used in a tool which i did wrapped and without it the tool can not be used in Galaxy. The only thing i know is that this file format is a binary format and was generate with a Rust program.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@github-actions github-actions bot changed the title Add bcsp datatype [24.1] Add bcsp datatype Dec 20, 2024
@github-actions github-actions bot added this to the 24.1 milestone Dec 20, 2024
@SantaMcCloud
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had a review here (#19363) just had to make the commit into this branch to have the dataype

@SantaMcCloud
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Hm okay i dont know why the test had an error

@bgruening
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Most likely not your fault.

@SantaMcCloud
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Most likely not your fault.

ah okay good to know then

@bernt-matthias
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What is the Linux file command telling you about this file? Can you ask the developers what these files are?

@SantaMcCloud
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SantaMcCloud commented Dec 21, 2024

(fairy_env) sf373@LAPTOP-7RMLPR2D:~/sf373$ file -i single_test.fasta.gz.bcsp 
single_test.fasta.gz.bcsp: application/octet-stream; charset=binary
(fairy_env) sf373@LAPTOP-7RMLPR2D:~/sf373$ file -c single_test.fasta.gz.bcsp 
cont    offset  type    opcode  mask    value   desc
(fairy_env) sf373@LAPTOP-7RMLPR2D:~/sf373$ file single_test.fasta.gz.bcsp 
single_test.fasta.gz.bcsp: data
(fairy_env) sf373@LAPTOP-7RMLPR2D:~/sf373$ 

This is the Linux output.

I also open a issuse asking about this format if they give me some information about it or a link to a source to read about

@SantaMcCloud
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@bernt-matthias i got an asnwer from the developer. This file is a binary format of the k-mer hash table which is only compatible with the tool Fairy.

@bernt-matthias
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Thanks for the efforts. Than I would only ask you to add a description attribute here. Then it should be good to go.

@SantaMcCloud
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Done!

@bgruening bgruening merged commit 33cabba into galaxyproject:release_24.1 Dec 28, 2024
42 of 48 checks passed
@bgruening
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thanks @SantaMcCloud

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This PR was merged without a "kind/" label, please correct.

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3 participants