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Adding a very simple dev script that creates .rda files out of our .tsv mapping data. Replaced a few places where the only raw TSV data was used instead of the internal datasets. Removed some S. epi files of uncertain origin. Not sure where those came from, honestly.
Updating scripts to use BiocFileCache throughout. Updating manifest for better handoff to amRml. Updating HMMER databases to use BiocFileCache and be saved as resources.
Wee `devtools::document(".")` updates, and adding BiocFileCache to Imports.
Error in `.runHmmerJob()`: ! unused argument (total_proteins = total_proteins) So if make the change, the error is not showing up. But I still don't know the logic.
Without this, clean_drug/drug_class/drug_abbr/class_abbr/cleaned_bvbrc_countries only resolve under devtools::load_all(); a real installed-package library() call throws object 'clean_drug' not found, which breaks runDataProcessing().
eboyer221
requested changes
Sep 15, 2026
Good catch Emily! Can replicate that `checkDataAvailability()` fails with this absent. Co-authored-by: Emily Boyer <130874527+eboyer221@users.noreply.github.com>
CPU resource detection was faulty on HPC. Added parallelly as an Import, and updated to use the recommended future CPU detection method, parallelly::availableCores(). This should behave better to avoid oversubscription on any system, and generally handle CPU requests more carefully.
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If something happened while downloading I would suggest having a check if it fails to press, go back and download at least once again. |
Abhirupa noted that HMMER DBs can corrupt on download or press, and get stuck in the mysterious BFC cache somewhere with no easy way to fix them. This adds a simple function to delete databases. Enjoy.
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BiocFileCachefor better handling of manifests and databases..tsvfiles instead of.rdaobjects.amRml.prepareGenomes("Staphylococcus argenteus")runDataProcessing("data/Staphylococcus_argenteus/Sar.duckdb")This will probably take a while, as it will download the HMMER databases freshly into your BiocFileCache data directory. The manifest
.jsonshould also have fun new things recorded, including a status message foramRmlto read.