view sort_bam.sh @ 7:90098d9cb691 default tip

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#!/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