How to build a command line package from scripts?

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I have spent time working on a bioinformatics project and produced numerous scripts and now I would like to use them for building a bioinformatics software that runs in the command line terminal, with the costumary manual and binary files. I would like to be able 1. to protect the code, 2. Make it fancy by not having to count with multiple scripts and 3. share the code with any one interested.

Since I don't really know where to start from, I would like to ask for orientation on the topic. I have been reading about script compilation and I think this could work, but I have scripts in three different coding languages, mainly python and bash, so I have not seen any tutorial on this specific case.

Any help as sharing resources (videos, manuals, software, etc.) or giving tips is appreciated. I know this is a VERY open question, so open answers are also welcome.

bioinformatics compilation package bash
1 Answers

You could use the python argparse library to build a command line application that accepts arguments and flags. With this method, you can provide flags for user input and run your different scripts, including the bash scripts, based on user input.

https://realpython.com/command-line-interfaces-python-argparse/

Similarly, you can do this in a bash script that provides the user with options and run your other scripts based on input.

https://www.redhat.com/sysadmin/arguments-options-bash-scripts

I'm not sure what you mean by protect the code? If you mean hide the code, as far as I know, you cannot easily hide bash and python code or turn them into binaries if you want to share the script.

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