Currently submitting co-allocated MUSCLE application is only possible using the XML JobProfile (compare QCG-SimpleClient). Beside the different job description format you have to end the qcg-sub command with the QCG keyword:

$ qcg-sub muscle.xml QCG

Example of co-allocated MUSCLE job

<qcgJob appId="MAPPER" xmlns:jxb="http://java.sun.com/xml/ns/jaxb" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
	<task persistent="true" taskId="task">
		<requirements>
			<topology>
				<processes processesId="one" masterGroup="true">
					<processesCount>
						<value>1</value>
					</processesCount>
	                			<candidateHosts>
            						<hostName>zeus.cyfronet.pl</hostName>
            		    			</candidateHosts>
				</processes>
				<processes processesId="two">
					<processesCount>
						<value>1</value>
					</processesCount>
		               	 		<candidateHosts>
            						<hostName>reef.man.poznan.pl</hostName>
            		    			</candidateHosts>
				</processes>
				<processes processesId="three">
					<processesCount>
						<value>1</value>
					</processesCount>
		               	 		<candidateHosts>
            						<hostName>hydra.icm.edu.pl</hostName>
            		    			</candidateHosts>
				</processes>
	
			</topology>
		</requirements>
		<execution type="open_mpi">
			<executable>
				<application name="muscle"/>
			</executable>
			<arguments>
				<value>Triangle.cxa.rb</value>
			</arguments>
			<stdout>
				<directory>
					<location type="URL">gsiftp://qcg.man.poznan.pl/~/output-${JOB_ID}-${TASK_ID}</location>
				</directory>
			</stdout>
			<stderr>
				<directory>
					<location type="URL">gsiftp://qcg.man.poznan.pl/~/error-${JOB_ID}-${TASK_ID}</location>
				</directory>
			</stderr>
			<stageInOut>
				<file name="Triangle.cxa.rb" type="in">
					<location type="URL">gsiftp://qcg.man.poznan.pl/~/Triangle.cxa.rb</location>
				</file>
                                <directory name="outputs" type="out">
					<location type="URL">gsiftp://qcg.man.poznan.pl/~/results-${JOB_ID}-${TASK_ID}</location>
				</directory>

		</stageInOut>
		</execution>
		<executionTime>
			<executionDuration>P0Y0M0DT0H10M</executionDuration>
		</executionTime>
	</task>
</qcgJob>