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uab-cgds-worthey / DITTO-UI

Easy to use web interface for biologists to look for genetic variants and understand their deleteriousness using DITTO scores.
https://cgds-ditto.streamlit.app/
GNU General Public License v3.0
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Data connect #2

Closed wilkb777 closed 1 year ago

wilkb777 commented 1 year ago

Multiple updates are included in this PR:

  1. Switched to the use of a conda environment for managing dependencies, including Streamlit (this does not include testing of the deploy on streamlit cloud yet)
  2. Refactored several sections of the app for read-ability and modular design
  3. updated caching strategy for certain functions
  4. updated and added the formatted data of DITTO scores and essential variant information
  5. updated the README with updated setup and information on the project

Please test locally following the install and run instructions and verify functionality. Also review of logic and code base given the refactor will be good to do as well for this PR.

wilkb777 commented 1 year ago

That's a good catch. I've switched to using Mamba everywhere for this reason, the resolver for dependencies just works way better and much faster. I've updated the readme to reflect this fact for the local install and testing process. Sticking with mamba/conda for local dev will make life much easier for folks spinning it up on their machine for dev and testing.

Sadly it looks like folks have had issues with using Conda env files for deploys on Streamlit Cloud (see this issue discussion for more info). We'll want to tackle that in another PR and make sure to manage the deps in both files to keep them in sync.

tkmamidi commented 1 year ago

Followed the steps and everything is working as expected!