Closed nick-youngblut closed 1 year ago
Hi Nick, thanks for your comment! We used MUMmer with a version no older than 4.0.0rc1. However, I would not recommend using MUMmer directly to generate files needed for GT-Pro database building since MUMmer output has to be processed to feed the downstream building. We had another tool called Maast (https://github.com/zjshi/Maast.git), old name CallM, to make it a little bit easier. I've updated the tool name in the docs.
We had another tool called Maast (https://github.com/zjshi/Maast.git), old name CallM, to make it a little bit easier. I've updated the tool name in the docs.
...and I just got CallM working in my pipeline 🤣
CallM was very light on docs, but I see that Maast has quite a bit. I'll give it a go!
@zjshi If you'd like, I could submit a PR for Maast that includes a github CI yaml to help with testing the installation (and run any application/unit tests).
My apologies for the outdated docs in GT-Pro docs... and thanks for trying Maast, too! For Maast github CI yaml, do you mean something different than what in conda_recipe/meta.yaml
(https://github.com/zjshi/Maast/blob/main/conda_recipe/meta.yaml)?
For Maast github CI yaml, do you mean something different than what in conda_recipe/meta.yaml
I mean a github workflow (e.g., https://github.com/zjshi/gt-pro/blob/master/.github/workflows/ci.yaml). It wouldn't take much to adapt the gt-pro workflow for maast.
I highly recommend github workflows for testing installs, running application & unit tests, and automated release publishing
It would be great if you provided the code that you used create both required files, versus gt-pro users reinventing the wheel for each custom database.
It would also be helpful to list this as a dependency at https://github.com/zjshi/gt-pro#additional-dependencies and state which versions of MUMmer4 are known to work correctly for generating the required files for gt-pro.