# HG changeset patch
# User biomonika <biomonika@psu.edu>
# Date 1410487282 14400
# Node ID ffe50d004cb4064808b83fba72802688f40dd304
# Parent  cf0d2b74769edc2331c1d476dab2fa0a1723b549
samtools sort, echo path

diff -r cf0d2b74769e -r ffe50d004cb4 sort_bam.sh
--- a/sort_bam.sh	Thu Sep 11 21:58:16 2014 -0400
+++ b/sort_bam.sh	Thu Sep 11 22:01:22 2014 -0400
@@ -3,5 +3,7 @@
 bam_file=$2;
 
 hash samtools 2>/dev/null || { echo "I require samtools in path but it's not installed.  Aborting."; exit 1; }
+echo $LINKYX_PATH
+echo $SAMTOOLS
 samtools sort $bam_file $results 2>log.txt