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changeset 24:cf0d2b74769e

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samtools_sort_debug
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 21:58:16 -0400
parents e3e22ba441c9
children ffe50d004cb4
files sort_bam.sh
diffstat 1 files changed, 1 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/sort_bam.sh	Thu Sep 11 20:26:05 2014 -0400
+++ b/sort_bam.sh	Thu Sep 11 21:58:16 2014 -0400
@@ -2,5 +2,6 @@
 results=$1;
 bam_file=$2;
 
+hash samtools 2>/dev/null || { echo "I require samtools in path but it's not installed.  Aborting."; exit 1; }
 samtools sort $bam_file $results 2>log.txt