Reordering code for non-sudo runs and preparation for singularity.

[Rudolph-afk]

slapnap utility functions wrapped in a package to be loaded when needed.

Run scripts moved to bin directory to be used as executables.

Updated Dockerfile to show new installation and of slapnap package and executatble scripts.

I have tested the application using examples from https://benkeser.github.io/slapnap/4-sec-examples.html as suggested by @bdwilliamson. All examples worked as intended but 2 main issues arose:

1. The viruses from CATNAP downloaded recently fail to be processed by the aa.char.2.vir.geom function in 02_multi_ab.R script.
2. Variable importance fails. I do not know if it is because of the parameters I provided or not as this part of the analysis is not available on examples.