  Soft gamma repeaters and anomalous X-ray pulsars are thought to be magnetars,
neutron stars with strong magnetic fields of order $\mathord{\sim}
10^{13}$--$10^{15} \, \mathrm{gauss}$. These objects emit intermittent bursts
of hard X-rays and soft gamma rays. Quasiperiodic oscillations in the X-ray
tails of giant flares imply the existence of neutron star oscillation modes
which could emit gravitational waves powered by the magnetar's magnetic energy
reservoir. We describe a method to search for transient gravitational-wave
signals associated with magnetar bursts with durations of 10s to 1000s of
seconds. The sensitivity of this method is estimated by adding simulated
waveforms to data from the sixth science run of Laser Interferometer
Gravitational-wave Observatory (LIGO). We find a search sensitivity in terms of
the root sum square strain amplitude of $h_{\mathrm{rss}} = 1.3 \times 10^{-21}
\, \mathrm{Hz}^{-1/2}$ for a half sine-Gaussian waveform with a central
frequency $f_0 = 150 \, \mathrm{Hz}$ and a characteristic time $\tau = 400 \,
\mathrm{s}$. This corresponds to a gravitational wave energy of
$E_{\mathrm{GW}} = 4.3 \times 10^{46} \, \mathrm{erg}$, the same order of
magnitude as the 2004 giant flare which had an estimated electromagnetic energy
of $E_{\mathrm{EM}} = \mathord{\sim} 1.7 \times 10^{46} (d/ 8.7 \,
\mathrm{kpc})^2 \, \mathrm{erg}$, where $d$ is the distance to SGR 1806-20. We
present an extrapolation of these results to Advanced LIGO, estimating a
sensitivity to a gravitational wave energy of $E_{\mathrm{GW}} = 3.2 \times
10^{43} \, \mathrm{erg}$ for a magnetar at a distance of $1.6 \, \mathrm{kpc}$.
These results suggest this search method can probe significantly below the
energy budgets for magnetar burst emission mechanisms such as crust cracking
and hydrodynamic deformation.
