Qfyilyi

myProgram takes three files as inputs, like so:

$ myProgram inputA inputB inputC

And say these inputs themselves reside in their own respective directories w/ some additional files:

directoryA

  inputA

  inputA_helperfile1

  inputA_helperfile2

directoryB

  inputB

  inputB_helperfile1

  inputB_helperfile2

directoryC

  inputC

  inputC_helperfile1

  inputC_helperfile2

myProgram will not run properly unless all three inputs as well as these additional files (dependencies? Is that the right term?) are in the same directory. But I do not want to put all these files into the same directory in order to execute myProgram. Is there a workaround for this scenario?

I am very new to bash (and programming/scripting in general), so please forgive me if this is a trivial question! (It is non-trivial to me, and I was unable to find an adequate answer by Googling for it.)

It might be easier to propose a good solution if you would explain what exactly myProgram is. Did you implement it?
Is it documented that it requires all files to be in one directory?
What happens if you call your program like this?

myProgram directoryA/inputA directoryB/inputB directoryC/inputC

If myProgram requires that all files are in the same directory, you could write a script that creates a temporary directory, changes the working directory into this temporary directory, copies all files there, executes myProgram inputA inputB inputC, leaves the temporary directory and removes it including all contents.

Instead of copying the files you can also create symbolic links in the temporary directory if your file system allows this.

You probably would implement your script to be called like this

myScript directoryA/inputA directoryB/inputB directoryC/inputC

You could use dirname and find to list all files from directory[ABC] if your program needs all files that reside in these directories. Otherwise you have to specify how to find out which of all the files are inputA_helperfile1 etc.

You may have to handle duplicate file names. If e.g. inputA_helperfile1 and inputB_helperfile1 would actually be the same file names with different content you cannot copy both files into the same directory.