updated Hadoop commands, absolutizing aligner conf path
updated Hadoop commands, absolutizing aligner conf path

thammegowda/incubator-joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,fhieber/incubator-joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,fhieber/incubator-joshua,fhieber/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua,thammegowda/incubator-joshua