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Add pod5 datatype #18419

Merged
merged 4 commits into from
Jun 26, 2024
Merged

Add pod5 datatype #18419

merged 4 commits into from
Jun 26, 2024

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TomHarrop
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I'd like to add the Oxford Nanopore binary Pod5 datatype to support the dorado wrapper I'm developing over here.

That PR also includes tool that can convert fast5.tar (already supported by Galaxy) to pod5.

pod5 has a fixed signature so the sniffer just checks for that.

Thanks!

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.

lib/galaxy/datatypes/binary.py Outdated Show resolved Hide resolved
lib/galaxy/datatypes/binary.py Show resolved Hide resolved
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Can we make this file smaller ?

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I subset it to one read and it's still 19K.

@TomHarrop
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@bernt-matthias @mvdbeek thanks for the reviews, I've made those changes.

@TomHarrop
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I can’t tell for sure if the test failures are related to my changes. Please let me know if I need to fix something in this PR.

@nsoranzo
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I can’t tell for sure if the test failures are related to my changes. Please let me know if I need to fix something in this PR.

All test failures are unrelated to your PR, thanks!

@nsoranzo nsoranzo merged commit 9524be3 into galaxyproject:dev Jun 26, 2024
46 of 52 checks passed
@TomHarrop TomHarrop deleted the datatype_pod5 branch June 26, 2024 08:16
@nsoranzo nsoranzo added this to the 24.2 milestone Jul 5, 2024
@bgruening
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@TomHarrop you can backport datatypes to the stable release, eg. 24.1

@TomHarrop TomHarrop mentioned this pull request Jul 7, 2024
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@TomHarrop
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Thanks @bgruening I tried to cherry-pick the commits into the release_24.1 branch here.

@galaxyproject galaxyproject deleted a comment from github-actions bot Jul 7, 2024
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5 participants