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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: bioconda/bioconda-recipes#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.
The text was updated successfully, but these errors were encountered:
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
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).
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: bioconda/bioconda-recipes#42751)
I have a few questions or suggestions.
Most importantly:
Other comments:
#!/usr/bin/env python
The text was updated successfully, but these errors were encountered: