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hgbrian / biomodals

bioinformatics tools running on modal
MIT License
60 stars 6 forks source link

Offer to add more bioinfo tools #2

Open tdsone opened 3 weeks ago

tdsone commented 3 weeks ago

Hi Brian,

I have a couple of bioinfo tools that I "ported" to modal (blat, STAR, https://github.com/tdsone/modal-rna-seq-pipeline). Do you think this would be useful in biomodals as well (biomodals seems pretty protein design centric for now)?

Love to get your feedback and if suitable, I would open a PR for each tool.

Cheers! Timon

hgbrian commented 3 weeks ago

Hey Timon, for better or worse, my philosophy is that each app should be one self-contained file: modal_{app}.py (I may add one shared utils.py file too). I would also like all apps to have a similar interface (e.g., use --input-pdb), but i haven't really achieved that.

There is also a bit of an effort to move this repo to modal-labs to make it a true managed community project, which is probably the true long-term solution. https://github.com/modal-labs/biomodals

Perhaps for now I can link to your repo in the README? Your repo has a lot of files and I don't know that you'd want to change it so much to fit into the mold of this repo. (If you do, then great!)

BTW it's great to know about your repo! I have run rnaseq pipelines recently, using nf-core, and it was really painful.

Best, Brian