This data managers fetches models (from the pangolin-data, pangolin-assignment and constellations repositories) for the pangolin SARS-CoV-2 lineage typing tool and updates the pangolin_data, pangolin_assignment and pangolin_constellations data tables.

The default is to fetch the latest version of the databases. If specific versions of databases need to be installed, a version compatibility matrix needs to be provided to help choose the versions available. This matrix is stored in a CSV file in the pangolin repository and can be downloaded at this link. When loading this file into Galaxy, the csv datatype needs to be selected, because the automatic format detection code detects this file as type txt.

Note that this data manager will only download database versions mentioned in the above mentioned file. While effort is taken to ensure that this file is updated with each pangolin database release, if that has not happened, the user of this data manager will need to provide their own version compatibility matrix file in order to load the latest database release into Galaxy.

The data manager will read the existing data tables and not re-download or replace databases that are already present in those data tables.