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Update Bakta & Fix errors with Bakta and AMRFinderPlus DB #6013

Merged
merged 3 commits into from
May 30, 2024
Merged

Update Bakta & Fix errors with Bakta and AMRFinderPlus DB #6013

merged 3 commits into from
May 30, 2024

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bebatut
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@bebatut bebatut commented May 17, 2024 •
edited

FOR CONTRIBUTOR:

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

Hi,

This PR updates Bakta and (hopefully) fixes some errors that we got with Bakta:

Bérénice

@bebatut bebatut force-pushed the bakta_update branch 2 times, most recently from f4cb7f6 to c4e1b3d Compare May 21, 2024 08:32
bgruening
bgruening reviewed May 21, 2024
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tools/bakta/test-data/V5.1_light_2024-01-19/amrfinderplus-db/2024-05-02.2/AMRProt.phr Outdated
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This one seems to be too big.

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@bebatut bebatut May 21, 2024 •
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I know. I just could not find out how to reduce it...

tools/bakta/test-data/V5.1_light_2024-01-19/amrfinderplus-db/2024-05-02.2/AMRProt.psq Outdated
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This one is even bigger.

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bebatut commented May 22, 2024 •
edited

To do in the PR

  • Remove AMRFinderPlus DB in Bakta DM
  • Create a small Bakta DB for tests in Bakta DM that will be stored on Zenodo
  • Create a small AMRFinderPlus DB:
    • Download BDD from NCBI ftp
    • Downsample FASTA files
    • Run AMRFinderPlus DM to build indexes and other files
  • Use versioned AMRFinderPlus data table
  • Add filter on AMRFinderPlus DB version

@bebatut bebatut force-pushed the bakta_update branch 2 times, most recently from ae6bd46 to d3ce835 Compare May 29, 2024 08:10
@bebatut
Fix Bjoern's comment
895530c 
- Remove print in python
- Replace some name inputs by argument
- Replace all test-data outputs by assert_contents
- Remove test-data outputs
clsiguret
clsiguret reviewed May 30, 2024
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This looks good for me 👍
Thanks for doing it 😀

@bgruening bgruening merged commit e277883 into galaxyproject:main May 30, 2024
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Thanks :-)

@bebatut bebatut deleted the bakta_update branch May 30, 2024 12:26
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@bgruening bgruening bgruening approved these changes

@clsiguret clsiguret clsiguret approved these changes

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@bebatut @bgruening @clsiguret