Call_metaphlan.shx

#!/bin/bash

set -e

DIR=Metaphlan_output
job=Metaphlan_Primates
email=alon.shaiber@gmail.com
WAIT () {
    python /workspace/meren/wait_for_cluster.py $1
}

LOG () {
    msg="[`date`] $1"
    echo $msg >> $job-log.txt
    echo $msg | mail -s "Update on $job" $email

}

CALL_MET () {
        sample=$1
        R1=$2
        R2=$3
        clusterize -log $DIR/$sample\_metaphlan_profile.txt metaphlan2.py $R1,$R2 --bowtie2out $DIR/$sample\_bowtie2.bz2 --nproc 5 --input_type fastq
}
LOG Hi!
LOG `echo $mpa_dir`
while read sample R1 R2;do
        if [ "$sample" == "sample" ]; then continue; fi
        CALL_MET $sample $R1 $R2
done < samples.txt
WAIT metaphlan2.py
LOG "All done!"