Mercurial > repos > biomonika > linkyx
diff sort_bam.sh @ 2:0d8315be76b7
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author | biomonika |
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date | Tue, 17 Feb 2015 21:59:51 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sort_bam.sh Tue Feb 17 21:59:51 2015 -0500 @@ -0,0 +1,10 @@ +#!/bin/bash +results=$1; +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:" $LINKYX_PATH +echo "SAMTOOLS:" $SAMTOOLS +echo "PATH:" $PATH +samtools sort $bam_file $results 2>log.txt +