Command line interface (CLI)

loculus-project / loculus

An open-source software package to power microbial genomic databases

https://loculus.org

GNU Affero General Public License v3.0

34 stars 1 forks source link

Open chaoran-chen opened 3 days ago

chaoran-chen commented 3 days ago

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 commented 3 days ago

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)