ASSEMBLY=hg19

mkdir -p ~/data/ucsc-data/${ASSEMBLY}

wget -O ~/data/ucsc-data/${ASSEMBLY}/chromInfo.txt.gz  http://hgdownload.cse.ucsc.edu/goldenpath/${ASSEMBLY}/database/chromInfo.txt.gz
wget -O ~/data/ucsc-data/${ASSEMBLY}/refGene.txt.gz  http://hgdownload.cse.ucsc.edu/goldenpath/${ASSEMBLY}/database/refGene.txt.gz

workon stuff
~/Downloads/spark-1.6.1/bin/spark-submit create_gene_counts.py ${ASSEMBLY}
