#!/bin/bash
SDIR="$( cd "$( dirname "$0" )" && pwd )"
if [ "$#" -ne 2 ]; then
echo "usage processMapFile.sh GENOME MAPPING_FILE"
exit
fi
GENOME=$1
MAPPING=$2
for sample in $(cat $MAPPING | cut -f2 | sort | uniq); do
echo $sample;
cat $MAPPING | awk -v S=$sample '$2==S{print $4}' \
| xargs bsub -o LSF.CONTROL/ -J S1Seq__${sample}__$(basename $MAPPING | sed 's/_sample_map.*//') \
-R "rusage[iounits=0,mem=1]" \
$SDIR/pipe.sh $GENOME $sample
done