Open paulzierep opened 3 months ago
Got this from the docs: https://eukulele.readthedocs.io/en/latest/databaseandconfig.html
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
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 inparams["output_data"][0]["extra_files_path"]
.Tell the tool to use
--reference_dir
and point to the location stored in the loc file.