Conda/pip/Galaxy are all easier ways to install Deeptools. See https://deeptools.readthedocs.io/en/develop/content/installation.html

You can install using:

pip install deeptools

It is unprofessional that the only type of installation they describe in detail on the GitHub page can't be done because the setup file is missing. That said, a little bit of extra reading - finding a sentence that reads "There are many easy ways to install deepTools. Details can be found here" - will easily get you to other ways of installing the package.