I am trying to run the genome browser mango that is being developed on top of Adam.
https://github.com/bigdatagenomics/mango
After installing it as recommended:
$ git clone https://github.com/bigdatagenomics/mango.git
$ cd mango
$ mvn clean package -DskipTests
I get an error when trying to execute the mango-submit command locally
bin/mango-submit -h
Exception in thread "main" java.lang.NoClassDefFoundError: org/eclipse/jetty/server/Handler
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:340)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:633)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:169)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:192)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:111)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jetty.server.Handler
at java.net.URLClassLoader$1.run(URLClassLoader.java:372)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:360)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 7 more
I suspect this has something to do with a conflicting java or scala version, or something similar. But I am not sure because it is mentioned in the documentation that mango includes all necessary dependencies. And it looks like it does download all the dependencies when building using maven.
I tried changing the java version in the mango pom file to the one that I use system-wide; 1.8. But that doesn't fix the problem. Changing the scala version to the one that I have system wide prevents the build from finishing (Could not find artifact org.scalatest:scalatest_2.11:jar:1.9.2)
I am able to execute adam-submit, spark-submit and both the adam and spark shells.
Any suggestions?
