I've merged the pull request with the initial Rocchio implementation. This isn't final, but I'd like to get a first pass.

You'll need to update your Maven dependencies. You should be able to run "mvn package -U".  Make to make sure that you have the right version of irutils:

ls -al ~/.m2/repository/edu/illinois/lis/ir-utils//0.2.0-SNAPSHOT/*

You should see ir-utils-0.2.0-20170630.185648-5.jar. If not, delete the contents of the 0.2.0-SNAPSHOT directory and run mvn package again.

I've also added the lucene/rocchio.sh runer to the biocaddie repo.  Like RM3, this will create a lot of output files (>9000). I recommend that you run this on the NCSA server – biocaddie.ndslabs.org – since it has 32 cores.  Because of disk space issues, you'll want to store your results in /data/thphan (I created a directory for you).

Since this is a new implementation, there may be problems. You can either email me or assign the ticket to me if you get blocked.