load samtools

[uiuc_igb_scripts.git] / fpkm_from_srr

diff --git a/fpkm_from_srr b/fpkm_from_srr
index a7ab6e0a4ef9c03c818c9737f1c0a810cc7b87f8..4f75cf370bacd0f2296d5a28d16f43c572bcd327 100755 (executable)
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -9,6 +9,7 @@ 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/0.1.18
     (cd $FROM_SRR_SRR;
      fastq-dump ${FROM_SRR_SRR}.sra;
      bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;