Add support for pyfamsa and pytrimal

[jonas-fuchs]

Dear Maintainers,

I do not know how easy this is. Both packages are cython ports of bioinformatic tools (alignment and trimming). It is from the same maintainer with similar repo structures, so I thought one issue might be enough. I actually struggled to get it running via shinylive, so I hope I am correct here. I tried to install with micropip and even make my own wheel (with both I failed, probably because I no prior experience with pyodide). Hope, you can be of help or give me some pointers!

Kind regards,
Jonas

🐍 Package Request

• Package Name and Version: pyfamsa>=0.5.3, pytrimal>=0.8.1
• Package URL: https://github.com/althonos/pytrimal https://github.com/althonos/pyfamsa
• Package Dependencies that needs to be resolved first: scoring-matrices~=0.3.0 (https://github.com/althonos/scoring-matrices)

Checklists

• I have tried to install the package using micropip.install(...) and encountered the issue.
• I have read the documentation and tried building the package myself.

[agriyakhetarpal]

Hi @jonas-fuchs, thanks for reaching out! The approach here would be to build the FAMSA2 and trimAl libraries first and add their recipes, and pass the paths to the libraries to the Cython packages for linkage. There are a lot of recipes for static and shared libraries in the packages/ folder, and they can be used as a reference for how to write your own recipes. Here are the docs: https://pyodide.org/en/stable/development/building-packages-using-recipe.html#building-packages-using-recipe

It you could open a PR, we would be happy to help you with your queries and debug build issues. :) However, if there are issues that are not specific to Pyodide but related to compilation to WASM in general, those would be best answered by the maintainers of FAMSA2/pyfamsa and/or trimAl/pytrimal – it might also be useful to reach out to their maintainers at some point to see if they could potentially act as recipe maintainers for us and help us diagnose build issues.

[jonas-fuchs]

I ll give it a try