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bpt26 / usher_wiki

docs holder for usher wiki
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Update Tutorial to use Taxoniumtools #10

Closed theosanderson closed 1 year ago

theosanderson commented 1 year ago

This was prompted by this nice blog which reads:

| Although the UShER wiki recommends matUtils extract to produce a MAT for Taxonium visualization, Taxonium recommends taxoniumtools to do this conversion for current Taxonium Version 2.

It's probably easiest for new users to be pointed to Taxoniumtools (even though it's not at all perfect compared to matUtils extract in the V1 days!)

AngieHinrichs commented 1 year ago

Thanks Theo! Yes, we definitely should be recommending taxoniumtools. 🙂

One little thing, I think the && gunzip public-latest.metadata.tsv.gz at the end of this line is counterproductive because the usher_to_taxonium command uses the compressed form public-latest.metadata.tsv.gz:

wget http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/public-latest.metadata.tsv.gz && gunzip public-latest.metadata.tsv.gz
...
usher_to_taxonium --input public-latest.all.masked.pb --output public-latest-taxonium.jsonl.gz --metadata public-latest.metadata.tsv.gz --genbank hu1.gb --columns genbank_accession,country,date,pangolin_lineage

[The && gunzip public-latest.all.masked.pb.gz could also be dropped but then the usher_to_taxonium command would need to be updated to use the .pb.gz.]

theosanderson commented 1 year ago

Agh - thanks so much for catching that!

What I've ended up doing here is keeping the protobuf compressed, since there is no advantage to unzipping it. But I've kept the TSV unzipped in case that inspires people to realise they can change it, add columns, etc.

Of course feel free to make whatever changes you want after merging :) Thanks again for the catch

AngieHinrichs commented 1 year ago

Great, thanks again! @bpt26 / @yatisht this looks good to me.

yatisht commented 1 year ago

I merged it. @amkram do you have merge privileges for this repo?

theosanderson commented 1 year ago

Thanks folks, sorry it looks like I've butchered the links. Rst is not my forte. I'll rudely leave the clean-up to someone with the power to merge 😳

(Should be fixed in https://github.com/theosanderson/usher_wiki/tree/patch-1, sorry again)

yatisht commented 1 year ago

Fixed it :)

theosanderson commented 1 year ago

Thank youuuu

amkram commented 1 year ago

Thanks for adding this!

@yatisht I don't think I have merge access, but if you are able to invite me that would be great!

yatisht commented 1 year ago

I can't. @bpt26 could you please add @amkram as a collaborator on this repo?