I don't have matlab installed, but I can run it from octave just fine:
octave:1> unix('./graph-tool --version')
graph-tool 1.2.0devel (commit 57d3cff82dcfd91646abedb7627cbdcb353eae97)
Written by Tiago de Paula Peixoto <tiago(a)forked.de>
Copyright (C) 2007 Tiago de Paula Peixoto
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
ans = 0
The error message you got seems to be related to python itself, more
specifically to the gzip python module. Can you run other python
programs from matlab? Can you also run graph-tool from octave, as above?