Command line interface (CLI)

[chaoran-chen]

We would like to add a CLI for Loculus to download and submit sequences.

Any suggestions on how the interface should look like? And any preferences on the programming language, etc.?

[theosanderson]

IMO:

• Python
• Likely a single executable, similar to e.g. the GitHub CLI with something like pathoplexus upload --organism ebola-zaire --sequences my_seqs.fasta --metadata my_data.tsv (which would then prompt you for credentials, but also having a way to pass credentials)