Clarify GISAID CLI usage

CDCgov / seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

https://cdcgov.github.io/seqsender/

Apache License 2.0

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Closed nbx0 closed 7 months ago

nbx0 commented 1 year ago

[x] Clarify in documentation the need for users to go to gisaid.org and download their CLI-API, where to install it for SeqSender to use it and requesting their token.
[x] Refactor seqsender internal code to import their CLI python pkg and use their commands rather than the raw API. This will assure that changes made by GISAID get inherited to SeqSender more smoothly.

cc: @leebrian @rchau88 @kristinelacek

dthoward96 commented 1 year ago

Setting up a meeting with @rchau88 this week to go over how this could possibly impact the docker version

dthoward96 commented 7 months ago

GISAID users are notified to download GISAID CLI and load into seqsender. https://github.com/CDCgov/seqsender?tab=readme-ov-file#prerequisites