Mercurial > repos > biomonika > linkyx

view sort_bam.sh @ 32:cf7cd22fc5d3 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add changeset revisions for packages
author biomonika
date Tue, 10 Feb 2015 12:09:34 -0500
parents 0c7f60054ee3
children
line wrap: on
line source

#!/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