There are few documents about the Amazon EMR Java API usage, in case you are finding codes configuring and starting EMR job using Java, here are the codes I use:

(a brief official sample can be found here, the file contains the following code is Here)

The codes include 2 steps, 1 for debugging and 1 for my own job. You can delete the debugging one if you want. (The code is modified based on some code I borrowed online, which I forget where I found it…thanks to the original author).

public class EMRStarter {

	private static final String HADOOP_VERSION = "0.20";
	private static final int INSTANCE_COUNT = 2;
	private static final String INSTANCE_TYPE = InstanceType.M1Small.toString();
	private static final String FLOW_NAME = "EMR Test";
	private static final String BUCKET_NAME = "my-bucket";
	private static final String S3N_HADOOP_JAR = "s3://" + BUCKET_NAME + "/jar/InventoryStorageCost.jar"; // jar
	private static final String outputDir = "test";
	private static final String S3N_LOG_URI = "s3://" + BUCKET_NAME + "/log/" + outputDir;
	private static final String[] JOB_ARGS = new String[] { 
			"s3://path",
			"s3://path",
			"s3://path",
			"arg"
			};

	private static final List ARGS_AS_LIST = Arrays.asList(JOB_ARGS);
	private static final List DONE_STATES = Arrays.asList(new JobFlowExecutionState[] {
			JobFlowExecutionState.COMPLETED, JobFlowExecutionState.FAILED, JobFlowExecutionState.TERMINATED 
        });

	static AmazonElasticMapReduce emr;

	/**
	 * 
	 * The only information needed to create a client are security credentials * consisting of the AWS Access Key ID and
	 * Secret Access Key. All other * configuration, such as the service end points, are performed * automatically.
	 * Client parameters, such as proxies, can be specified in an * optional ClientConfiguration object when
	 * constructing a client.
	 * 
	 * @see com.amazonaws.auth.BasicAWSCredentials
	 * 
	 * @see com.amazonaws.auth.PropertiesCredentials
	 * 
	 * @see com.amazonaws.ClientConfiguration
	 */

	private static void init() throws Exception {
		File file = new File("AwsCredentials.properties");
		AWSCredentials credentials = new PropertiesCredentials(file);
		emr = new AmazonElasticMapReduceClient(credentials);
	}

	public static void main(String[] args) throws Exception {
		System.out.println("===========================================");
		System.out.println("Welcome to the Elastic Map Reduce!");
		System.out.println("===========================================");

		init();

		StepFactory stepFactory = new StepFactory();
		// create the debugging step
		StepConfig enableDebugging = new StepConfig().withName("Enable Debugging")
				.withActionOnFailure("TERMINATE_JOB_FLOW").withHadoopJarStep(stepFactory.newEnableDebuggingStep());

		try {
			// Configure instances to use
			JobFlowInstancesConfig instances = new JobFlowInstancesConfig();

			System.out.println("Using EMR Hadoop v" + HADOOP_VERSION);
			instances.setHadoopVersion(HADOOP_VERSION);

			System.out.println("Using instance count: " + INSTANCE_COUNT);
			instances.setInstanceCount(INSTANCE_COUNT);

			System.out.println("Using master instance type: " + INSTANCE_TYPE);
			instances.setMasterInstanceType(INSTANCE_TYPE);

			System.out.println("Using slave instance type: " + INSTANCE_TYPE);
			instances.setSlaveInstanceType(INSTANCE_TYPE);

			// Configure the job flow
			System.out.println("Configuring flow: " + FLOW_NAME);
			RunJobFlowRequest request = new RunJobFlowRequest(FLOW_NAME, instances);

			System.out.println("tusing log URI: " + S3N_LOG_URI);
			request.setLogUri(S3N_LOG_URI);

			// Configure the Hadoop jar to use
			System.out.println("tusing jar URI: " + S3N_HADOOP_JAR);
			HadoopJarStepConfig jarConfig = new HadoopJarStepConfig(S3N_HADOOP_JAR);
			System.out.println("tusing args: " + ARGS_AS_LIST);
			jarConfig.setArgs(ARGS_AS_LIST);

			// main step
			StepConfig stepConfig = new StepConfig(S3N_HADOOP_JAR.substring(S3N_HADOOP_JAR.indexOf('/') + 1), jarConfig);
			request.setSteps(Arrays.asList(new StepConfig[] { enableDebugging, stepConfig }));

			// Run the job flow
			RunJobFlowResult result = emr.runJobFlow(request);
			// Check the status of the running job
			String lastState = "";
			STATUS_LOOP: while (true) {
				DescribeJobFlowsRequest desc = new DescribeJobFlowsRequest(Arrays.asList(new String[] { result
						.getJobFlowId() }));

				DescribeJobFlowsResult descResult = emr.describeJobFlows(desc);

				for (JobFlowDetail detail : descResult.getJobFlows()) {
					String state = detail.getExecutionStatusDetail().getState();
					if (isDone(state)) {
						System.out.println("Job " + state + ": " + detail.toString());
						break STATUS_LOOP;
					} else if (!lastState.equals(state)) {
						lastState = state;
						System.out.println("Job " + state + " at " + new Date().toString());
					}
				}

				Thread.sleep(10000);

			}

		} catch (AmazonServiceException ase) {
			System.out.println("Caught Exception: " + ase.getMessage());
			System.out.println("Reponse Status Code: " + ase.getStatusCode());
			System.out.println("Error Code: " + ase.getErrorCode());
			System.out.println("Request ID: " + ase.getRequestId());
		}

	}

	/**
	 * 
	 * @param value
	 * 
	 * @return
	 */

	public static boolean isDone(String value) {
		JobFlowExecutionState state = JobFlowExecutionState.fromValue(value);
		return DONE_STATES.contains(state);
	}

}