Yes, I'm trying to create those recipes on the fly. User gives me all the paths that he thinks are needed to run the tool inside the container (he gives a file that contains those paths and I read them into an array). With those paths I can build the recipe. In the %setup section I will create the directories, in the %files section I will copy files and in the %post section I will create the links. So I don't really want to create a shell script, I do want to build the recipe with Perl. But I didn't want to talk about Singularity because I guessed most of the people here are not familiar with it. So I tried to simplify it to creating a shell script (aka the recipe) that creates those directories, copies files and creates links.
So if we moved to talk about recipes, the purpose of the Perl script is to build the recipe, based on all the paths that users thinks are needed for running his tool in the container. So the input is really the paths, as I explained, and the output is the recipe (aka the shell script).
So my question is still remains. Given the paths, I want to build some structure that I could easily extract all the files/links/directories and use them for creating the recipe file. If you think there is a better way of creating it, I'm all ears.
choroba's answer is a good start but I had some questions that I commented under it.

In reply to Re^4: Getting all subpaths from a path by ovedpo15
in thread Getting all subpaths from a path by ovedpo15

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