Resolve incompatible Python dependencies

[iainrb]

setup.py was using the latest stable release for dependencies without a version specified; this resulted in incompatible dependency versions. This commit changes some versions and ensures all dependencies have a version number specified, which resolves the issue.

We have already released this change in our fork at oicr/gsi/svtools; you may also wish to merge it into the original repo.

Happy to discuss further if you would like. Thanks for your work developing svtools.