module load sratoolkit/2.3.5-2;
module load bwa/0.7.10;
module load cufflinks/2.2.1;
- module load samtools/0.1.18
+ module load samtools/1.0;
(cd $FROM_SRR_SRR;
fastq-dump --gzip ${FROM_SRR_SRR}.sra;
bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;