# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410487096 14400
# Node ID cf0d2b74769edc2331c1d476dab2fa0a1723b549
# Parent  e3e22ba441c92f5d856fa426e8bed15990057163
samtools_sort_debug

diff -r e3e22ba441c9 -r cf0d2b74769e sort_bam.sh
--- 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