From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 18:24:25 +0000 (-0700)
Subject: stop immediately upon error
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=30101ccb6c6cc073a74378a9fef315ebad60ab12;hp=e3a076b12c9216f42d6b8ae13751696fa0f3cd52;p=uiuc_igb_scripts.git

stop immediately upon error
---

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;
     );