Question: Installing mango genome browser: NoClassDefFoundError: org/eclipse/jetty/server/Handler
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gravatar for William
2.3 years ago by
William3.9k
Europe
William3.9k wrote:

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 dependancies when building using maven.

I tried changing the java version in the mango pom file to the one that I use systemwide; 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?

 

mango adam • 1.1k views
ADD COMMENTlink written 2.3 years ago by William3.9k
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