Pip-installing CNVkit from dxapp.json doesn't work; do it within the app script

For reasons not yet fully understood, the dxapp pip invocation will try to
install the latest versions of numpy and matplotlib, disregarding that
acceptable versions of both have already been installed. Then, matplotlib fails
to find the freetype2 library, and the reinstallation fails. WTF. None of this
happens when pip-installing from within the script. Maybe DNAnexus uses weird
pip arguments that force the updates.
Mostly there