function actually_run_the_alignment {
module load sratoolkit/2.3.5-2;
module load bwa/0.7.10;
module load cufflinks/2.2.1;
module load samtools/1.0;
function actually_run_the_alignment {
module load sratoolkit/2.3.5-2;
module load bwa/0.7.10;
module load cufflinks/2.2.1;
module load samtools/1.0;