App for submit CLI programs like AlphaFold2?

Hi, I plan to build an entry to submit CLI programs like AlphaFold2, wondering whether “job composer app” is a good starting point to customize.

This web entry enables users to:

  1. Fill app-related fields like input files, extra options.
  2. Submit jobs.

Any suggestion is appreciated.

Hi and welcome!

I only wish the job composer were a good app to start with. Sadly I’m not sure if it is. It doesn’t have the same web form → job submission capability you’re looking for (like the batch connect apps in the dashbaord) and IIRC it has shims in place for blocks of code that use old libraries - so that’s a recipe for either confusion or worse using those old libraries which could cause maintenance burdens.

You can check out this Rails app we deploy at OSC for the specific use case of submitting jobs to a specific program (in this case autodesk Maya). In it you manage projects, submit scripts (through a web form) and then manage those jobs.

Eventually the job composer will be a lot more flexible to allow YAML defined forms like batch connect apps, but as we haven’t even started that work, it’s quite a ways out.

For AlphaFold2, you could use the Jupyter Notebook app, which would allow you to start a job with proper resources. Then within that you could give your users an “AlphaFold notebook”, which is prepopulated with info on how to run the program. Not sure if this would be applicable to non-Python software.

That would appear to be similar to the Colab notebook they link to on their GitHub README (Google Colab). My thought was to use something like the “Making a Prediction” section of that notebook.

We’re not doing this at our site but this is what came to mind. Good luck!