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Minamehr / EUKulele

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Create data manager for EUKulele #1

Open paulzierep opened 5 months ago

paulzierep commented 5 months ago

The steps involved for DM are:

Finding out where EUKulele download --database phylodb installs the DB; copy the data from there to the location Galaxy needs (example: https://github.com/galaxyproject/tools-iuc/blob/3c6cc780d2d8ea156d167289cc2576fc3e43d2fd/data_managers/data_manager_mapseq/data_manager/data_manager_fetch_mapseq_db.py#L75-L87) which is in params["output_data"][0]["extra_files_path"].

Tell the tool to use --reference_dir and point to the location stored in the loc file.

paulzierep commented 5 months ago

Got this from the docs: https://eukulele.readthedocs.io/en/latest/databaseandconfig.html

paulzierep commented 5 months ago

I think the output of the DB can be assigned with --out_dir: https://github.com/AlexanderLabWHOI/EUKulele/blob/9ecd10bc16355cde3f12c1f355b4fc0b3b7c153d/src/EUKulele/EUKulele_main.py#L73C32-L73C41

paulzierep commented 5 months ago

Docs: https://docs.galaxyproject.org/en/latest/dev/data_managers.html