import compbio.engine.ClusterJobId;\r
import compbio.engine.Configurator;\r
import compbio.engine.SyncExecutor;\r
-import compbio.engine.client.ClusterNativeSpecExecutable;\r
+\r
import compbio.engine.client.ConfiguredExecutable;\r
import compbio.engine.client.Executable;\r
import compbio.engine.client.PathValidator;\r
* If executable require special cluster configuration parameters to\r
* be set e.g. queue, ram, time etc\r
*/\r
- if (confExec.getExecutable() instanceof ClusterNativeSpecExecutable<?>) {\r
- setNativeSpecs(confExec.getExecutable());\r
- }\r
+ setNativeSpecs(confExec.getExecutable());\r
+\r
\r
log.trace("using arguments: " + jobtempl.getArgs());\r
this.confExecutable = confExec;\r
}\r
\r
void setNativeSpecs(Executable<?> executable) throws DrmaaException {\r
- jobtempl\r
- .setNativeSpecification(((ClusterNativeSpecExecutable<?>) executable)\r
- .getNativeSpecs());\r
+ String nativeSpecs = executable.getClusterJobSettings(); \r
+ if(!compbio.util.Util.isEmpty(nativeSpecs)) {\r
+ log.debug("Using cluster job settings: " + nativeSpecs);\r
+ jobtempl.setNativeSpecification(nativeSpecs);\r
+ }\r
}\r
\r
void setEmail(String email) {\r