We are constructing a bacterial pathogen workflow and stick to the described documentation. While the tree is diplayed properly, we struggle to view the map in general (not the greyed option described in other posts).
We are currently running everything with default settings, we do not use a config-file. In this, there are 2 panels listed (tree and entropy). We have the country field defined in the metadata for each strain. Additionally, we have a lat-lon.tsv file directly from the bioinformatics documentation. Does the map require an additional command? or is it automatically generated when country is given in the meta-data file?
We also dont know how to build the auspice config file. Can you give us any hints? Is there a documentation?
If you need any more information, please specifiy.
For the map to be displayed showing country data the dataset (often called “Auspice JSON”) needs:
(i) The "geo_resolutions" to include “country”. This can be supplied via an auspice-config JSON or by adding --geo-resolutions country to augur export
(ii) The “country” to be exported as data. If you can select “country” as a color-by for the tree then this is already happening. If not, you should either define a coloring option in the auspice-config JSON or add --metadata-color-by country to augur export.
(iii) If the "panels" are explicitly defined within the dataset JSON, they must include “map”. You can just ignore this to start and Auspice will display everything it can.
The best place to learn about the auspice-config JSON is by looking at examples, e.g. zika is a minimal example which defines a map showing both country + region (~continent) level data. I would think you could copy that and make some minor modifications. There’s also a JSON schema. We have various docs related to this file as well, but there’s no single page which details everything; perhaps this would be the best place to start.