# HG changeset patch
# User iuc
# Date 1523399989 14400
# Node ID e798c0b3384cee09d4ea3799bf4958af790c2f2a
# Parent  fcc6efc4ef6d2762f2c7becf90c0f75463ab309f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c

diff -r fcc6efc4ef6d -r e798c0b3384c bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Tue Jan 23 12:20:00 2018 -0500
+++ b/bowtie2_wrapper.xml	Tue Apr 10 18:39:49 2018 -0400
@@ -9,6 +9,8 @@
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+## Use pipefail if available to quit with first non-zero exit code
+set -o | grep -q pipefail && set -o pipefail;
 ## prepare bowtie2 index
 #set index_path = ''
 #if str($reference_genome.source) == "history":