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Add database to Seroba recipe #35378
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Grabbed Test data from https://github.com/sanger-pathogens/pathogen-informatics-training/tree/master/Notebooks/SEROBA/data/run_seroba Testing Conda
Forgot to build db! brb |
ran into issue with latest KMC version
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Round 2! Conda
Super close, just need to fix the bcftools/pysam issue |
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Round 3 Conda
Conda looks good, test docker now Docker
Looks like seroba creates a temp tile at the entry point |
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Round 4 Conda
Conda looks good still Docker
Bummer, at this point this extends outside the scope of Seroba, as now I've submitted a PR to fix the pymummer recipe: #35379 |
Submitted upstream PR to help fix the temp dir issue: sanger-pathogens/seroba#68 Unsure of a timeline of review for this PR |
Have to update Ariba dependencies to get this working #35383 |
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Round 5 Conda
Now the test.... Docker
Last test, docker with Docker with
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Nice work, also liking that you've documented your attempts in fixing things :-)
@BiocondaBot please merge |
Sorry, this PR cannot be merged at this time. |
@BiocondaBot please merge |
I will attempt to upload artifacts and merge this PR. This may take some time, please have patience. |
Thank you! |
The database for Seroba is included in the repository (https://github.com/sanger-pathogens/seroba/tree/master/database) and is only 150 MB in size.
This PR adds the database to the recipe, and defaults to it. Users still have the option to provide their own database.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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