Which programming languages should I use to integrate different analysis software packages?
If you are mostly stitching up together calls into other software, like unix utilities (awk, grep, sed ...), python, and matlab scripts, bash is just fine or possibly even best for the job to construct simple pipelines and workflows.

It's easy in bash to read user input, store it in variables, then launch other software depending on the set variables. It's perfectly fast enough for that, and nothing else gets any easier.

If you, however, were to use bash for preprocessing itself, like looping through files line by line, packing and unpacking tab-separated values into arrays etc., that would be excruciatingly slow and not recommended.