I git-cloned Qiime into ~/src. I installed with --prefix=/home/username/local and then had to change the line in ~/.qiime_config to qiime_scripts_dir <tab> /home/username/local/bin.
In my ~/src I git-cloned qcli and installed it with --prefix=/home/username/local. I had to add /home/username/local/lib/python2.7/site-packages, /home/username/local/bin, and /home/username/local/lib to my $PYTHONPATH.
I also had to load the module matplotlib.