For this to work, the config file needs to have an entry for the wrapperpath added to each processing host array entry like this:
$PROCESSING_HOSTS[] = array('host' => 'guppy.scripps.edu',
'nproc' => 8,
'nodesdef' => '2',
'nodesmax' => '8',
'ppndef' => '8',
'ppnmax' => '8',
'reconpn' => '8',
'walltimedef' => '2',
'walltimemax' => '2',
'cputimedef' => '2',
'cputimemax' => '2',
'memorymax' => '30',
'appionbin' => '/opt/myamisnap/bin/appion/',
'baseoutdir' => DEFAULT_APPION_PATH,
'localhelperhost' => 'guppy.scripps.edu',
'dirsep' => '/',
'wrapperpath' => '/opt/myamisnap/bin/appion' );
USE_APPION_WRAPPER must still be defined as true for the paths to be added to commands.
If the wrapperpath entry is not defined for a host in the config file, no path will be added to a command even if USE_APPION_WRAPPER is true.