Conda packaging and galaxy tool

[bernt-matthias]

I'm currently considering including PepNet in Galaxy, i.e. to add a Galaxy tool. For this, a conda package for Pepnet would be required. I could work on both (actually I already started: https://github.com/bioconda/bioconda-recipes/pull/42751)

I have a few questions or suggestions.

Most importantly:

• The tensorflow addons python library is marked as deprecated (https://www.tensorflow.org/addons). Also its not available in conda-forge (which would be a requirement for the Galaxy platform) and I guess conda-forge would not be keen on incorporating deprecated python packages. Would it be possible to replace this?

Other comments:

• would be cool to have the first line #!/usr/bin/env python
• A versioned release via github would be appreciated (e.g. zenodo is fine but it does not allow to download the complete package and also has problems with DOS line endings)
• Create a pepnet module containing utils and the two python scripts (simplifies installation next to other python libraries)
• would be cool to have this pip installable, e.g. by creating setup.py or a project toml file.

[lkytal]

Thanks for your message. The TensorFlow addons package is used for training only, I can remove it from the conda package. For better structure, I'm considering creating a new repository to host the conda package, I'll let you know when I finished

[bernt-matthias]

For now it would be sufficient to remove tensorflow addons and to create a versioned release for this repository.

I'm considering creating a new repository to host the conda package

Since (out of the box) Galaxy only supports conda-forge and bioconda it would be better to have the package there (the linked PR to bioconda would do this).