From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 17:09:21 +0000 (-0700)
Subject: we want samtools 1.0, not samtools 0.1.8
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=0e5f3745f8f445db4cc77967c3baa0ed25362e97;p=uiuc_igb_scripts.git

we want samtools 1.0, not samtools 0.1.8
---

diff --git a/fpkm_from_srr b/fpkm_from_srr
index abcf486..27cad20 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -9,7 +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
+    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;