Questions from a custom Nextstrain builder

[abattenhouse]

As an outside user performing custom Nextstrain builds (for the Texas Department of State Health Services), I have a couple of questions. As background, I configure multiple builds using multiple input files.

1. I've noted that dropping a JSON file on auspice.us does not render the Frequencies panel. Why is this, and is there a way to get that information incorporated in the auspice.us rendering?

2. The tutorial documentation (and the advanced customization example build) use a colors.tsv file, but now a combination of color_ordering.tsv and color_schemes.tsv are used. Can a colors.tsv-style file specifying both the location and the specific colors still be used? If so, how? Just as a files: entry (top-level or under a build)?

3. I would like to configure initial custom top-level description file that appears when I invoke http://localhost:8888. (e.g. like the nextstrain_profiles/nextstrain-gisaid/nextstrain_description.md that you see for the global Nextstrain build. How do I do that? The contents of the description file I configure just show up on individual build pages.

Thanks for your help,
Anna Battenhouse
Center for Biomedical Research Support
The University of Texas at Austin

[jameshadfield]

I've noted that dropping a JSON file on auspice.us does not render the Frequencies panel. Why is this, and is there a way to get that information incorporated in the auspice.us rendering?

You will need to drag and drop both the main dataset JSON (e.g. X.json) and the tip-frequencies sidecar (X_tip-frequencies.json). Furthermore the "panels" section of the main JSON will need to include "frequencies", which is the default setting in the ncov workflow, so this should be ok.

Can a colors.tsv-style file specifying both the location and the specific colors still be used? If so, how? Just as a files: entry (top-level or under a build)?

Yes - see this line in the workflow which works out which input source to use for colours. The default is to use a rule which combines the ordering of traits (color_ordering.tsv) and then assigning a colour to each entry (color_schemes.tsv). But if you specify a TSV path in your builds.yaml via either builds -> {buildName} -> colors or files -> colors then your custom colour pairings will be used instead.

I would like to configure initial custom top-level description file that appears when I invoke http://localhost:8888/.

To do this you'll need to write your own custom auspice splash page and use this as a built-time customisation for auspice. This is what nextstrain.org does.

P.S. Really nice to hear the Texas Department of State Health Services is using Nextstrain 😄

[abattenhouse]

Thanks for all the great feedback James! Really appreciate it!

You know, I tried dropping the tip-frequencies JSON in auspice.us before mentioning it in the issue, and got an error about only being able to parse CSV files. I now realize that I need to drop both the main JSON and the tip-frequencies at the same time, since a file added later is interpreted as custom metadata.

I hope this info will be in your updated documentation, including the add-metadata-via-CSV capability which I only learned about through the CDC Gen Epi toolkit modules (I didn't see it in your documentation, although I believe I've read it all :)

Cheers, Anna

[jameshadfield]

Yeah - auspice.us was a side-project for a long time, but it's great to see how much it's being used! With that in mind, I recently wrote up some ideas to improve the UI when you are loading files at nextstrain/auspice.us#25. Comments welcome 😄

I hope this info will be in your updated documentation, including the add-metadata-via-CSV capability...

https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/drag-drop-csv-tsv.html