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The first issue is most likely caused by the fact that ~/.local/bin is not in the user's PATH environment variable. When you do a non-user-specific pip install the executables will get put into /usr/local/bin which is likely on your path by default (the same is true with an apt-get install although it will likely be in /usr/bin).
The second issue (where you provide full path to the executable) is because Python can't find modules that catkin_tools depends on. This is most likely because ~/.local/lib/python2.7/site-packages (and possibly ~/.local/lib/python2.7/dist-packages) are not on the user's PYTHONPATH environment variable. In global pip installs and apt-get installs, this would also not be an issue.
Try fixing those two environment variables for the user, and the issues should go away.
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