Since we are releasing a new version of biojava that introduces a number of API changes, I would like to suggest a review of some of the command line (CLI) tools that we have.

To my knowledge, we currently have CLI tools for the structural alignment algorithms and some symmetry analysis. The fist ones are implemented using a custom UserArgumentProcessor class. The second ones are implemented in a module of a separate repository called symmetry-tools.

The idea would be to have a more systematic way to create scripts (packaged as jar files) that can be distributed as standalone programs with the only requirement of java. An idea would be to split the algorithms (the computation code) and the command line interfaces (main methods) by creating a separate package called biojava-tools (for example), which depends on all the rest of biojava projects and special dependencies for the management of specific CLI tasks (like commons-cli).

Another possible option is to move the CLI scripts to a separate repository.