Mercurial > repos > biomonika > linkyx

diff sort_bam.sh @ 26:0c7f60054ee3

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toolshed perl, newest commit, two occurencies - based on toolshed bioperl
author biomonika <biomonika@psu.edu>
date Fri, 12 Sep 2014 00:23:56 -0400
parents ffe50d004cb4
children
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--- a/sort_bam.sh	Thu Sep 11 22:01:22 2014 -0400
+++ b/sort_bam.sh	Fri Sep 12 00:23:56 2014 -0400
@@ -3,7 +3,8 @@
 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
+echo "LINKYX_PATH:" $LINKYX_PATH
+echo "SAMTOOLS:" $SAMTOOLS
+echo "PATH:" $PATH
 samtools sort $bam_file $results 2>log.txt