I would pursue installation through Ambari, you will have a much easier time. Try the suggestion from @asubramanian and if you still run into issues, let us know and we'll help you through it and/or fix bugs if necessary.
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Can you provide more details? Specifically around why Elasticsearch is down? Did it install successfully? Are there errors in the ES logs? Are you able to interact with it directly (outside of Kibana)?
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There is also a metron_rest_classpath parameter that can be used for the same purpose (both of these parameters are added to the REST application classpath). You might want to consider keeping just /path/to/metron-elasticsearch-*-uber.jar in metron_indexing_classpath and moving the others to metron_rest_classpath. Probably won't matter now but could cause issues down the road if metron_indexing_classpath is ever reused for something else.
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When cloning and building Metron locally you have to be careful about adding extra files within your local copy. There is a plugin that runs (Apache Rat) that checks for licenses whenever you build. You likely added some files that don't have license headers and your best bet is to remove the files flagged in /path/to/metron/target/rat.txt.
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