From 30101ccb6c6cc073a74378a9fef315ebad60ab12 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 11:24:25 -0700
Subject: [PATCH] stop immediately upon error

---
 fpkm_from_srr | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 82e4ae9..9a310e5 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -3,6 +3,7 @@
 CORES=8
 MAX_MEM="32GB"
 
+set -e;
 
 function actually_run_the_alignment {
     module load sratoolkit/2.3.5-2;
@@ -24,7 +25,6 @@ function set_up_the_run {
     FROM_SRR_GTF="$3"
     export FROM_SRR_SRR FROM_SRR_GTF FROM_SRR_REF;
     mkdir -p "$FROM_SRR_SRR";
-    set -e;
     (cd $FROM_SRR_SRR;
      rsync -avP rsync://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/${FROM_SRR_SRR:0:6}/${FROM_SRR_SRR}/${FROM_SRR_SRR}.sra;
     );
-- 
2.39.2