We study the positivity and regularity of solutions to the fractional porous medium equations $u_t+(-Delta)^su^m=0$ in $(0,infty)timesOmega$, for $m>1$ and $sin (0,1)$ and with Dirichlet boundary data $u=0$ in $(0,infty)times({mathbb R}^NsetminusOmega)$, and nonnegative initial condition $u(0,cdot)=u_0geq0$. Our first result is a quantitative lower bound for solutions which holds for all positive times $t>0$. As a consequence, we find a global Harnack principle stating that for any $t>0$ solutions are comparable to $d^{s/m}$, where $d$ is the distance to $partialOmega$. This is in sharp contrast with the local case $s=1$, in which the equation has finite speed of propagation. After this, we study the regularity of solutions. We prove that solutions are classical in the interior ($C^infty$ in $x$ and $C^{1,alpha}$ in $t$) and establish a sharp $C^{s/m}_x$ regularity estimate up to the boundary. Our methods are quite general, and can be applied to a wider class of nonlocal parabolic equations of the form $u_t-mathcal L F(u)=0$ in $Omega$, both in bounded or unbounded domains.