Avocado cannot run with Hadoop 1.0.4.

[fnothaft]

Paging @massie

When we build avocado with Hadoop version set to 1.0.4 (necessary for default spark/ec2 deploy scripts), avocado throws an error:

Exception in thread "main" java.lang.NoSuchMethodError: org.codehaus.jackson.type.JavaType.<init>(Ljava/lang/Class;)V
    at org.codehaus.jackson.map.type.SimpleType.<init>(SimpleType.java:36)
    at org.codehaus.jackson.map.type.SimpleType.<clinit>(SimpleType.java:20)
    at org.codehaus.jackson.map.type.TypeFactory.<init>(TypeFactory.java:42)
    at org.codehaus.jackson.map.type.TypeFactory.<clinit>(TypeFactory.java:15)
    at org.codehaus.jackson.map.ObjectMapper.<clinit>(ObjectMapper.java:42)
    at org.apache.avro.Schema.<clinit>(Schema.java:80)
    at org.apache.avro.generic.GenericData.<clinit>(GenericData.java:862)
    at org.apache.avro.specific.SpecificDatumReader.<init>(SpecificDatumReader.java:31)
    at org.bdgenomics.adam.serialization.AvroSerializer.<init>(ADAMKryoRegistrator.scala:38)
    at org.bdgenomics.adam.serialization.ADAMKryoRegistrator.registerClasses(ADAMKryoRegistrator.scala:68)
    at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$2.apply(KryoSerializer.scala:64)
    at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$2.apply(KryoSerializer.scala:61)
    at scala.Option.foreach(Option.scala:236)
    at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:61)
    at org.apache.spark.serializer.KryoSerializerInstance.<init>(KryoSerializer.scala:116)
    at org.apache.spark.serializer.KryoSerializer.newInstance(KryoSerializer.scala:79)
    at org.apache.spark.broadcast.HttpBroadcast$.write(HttpBroadcast.scala:144)
    at org.apache.spark.broadcast.HttpBroadcast.<init>(HttpBroadcast.scala:44)
    at org.apache.spark.broadcast.HttpBroadcastFactory.newBroadcast(HttpBroadcast.scala:73)
    at org.apache.spark.broadcast.HttpBroadcastFactory.newBroadcast(HttpBroadcast.scala:69)
    at org.apache.spark.broadcast.BroadcastManager.newBroadcast(Broadcast.scala:95)
    at org.apache.spark.SparkContext.broadcast(SparkContext.scala:617)
    at org.apache.spark.rdd.NewHadoopRDD.<init>(NewHadoopRDD.scala:59)
    at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:471)
    at org.bdgenomics.adam.rdd.ADAMContext.adamParquetLoad(ADAMContext.scala:200)
    at org.bdgenomics.adam.rdd.ADAMContext.adamSequenceLoad(ADAMContext.scala:312)

@jey thinks this is some sort of dependency hell issue.

[fnothaft]

Closed by #85; upgraded Jenkins tester to run tests against Hadoop 1.0.4, 2.2.0, and 2.3.0.