#!/bin/bash
#PBS -l walltime=05:00:00
#PBS -l nodes=1:ppn=8
#PBS -l vmem=2000mb

#  runMACS.pbs.sh
#
#  Created by Ivory on 11/04/14.
#
# This is one of three components: callRunMACS.sh, runMACS.pbs, and MACStable.txt
# all three of these files (and the sample files) are necisary to run MACS.

# pass these variables via qsub
# IP=chipFile.bam
# INPUT=inputFile.bam
# NAME=sampleName

# activate the python 2.7 virtual environment
# btw, this post was very helpful:
# http://stackoverflow.com/questions/5506110/is-it-possible-to-install-another-version-of-python-to-virtualenv

source /home/ieclabau/virtualenvs/py2.7/bin/activate

cd $PBS_O_WORKDIR

G=119667750 # Arabidopsis
M=macs2 #path to MACS software--provided you are in the virtual python environment
Q=0.01
S=95 #peak shift

$M callpeak -f BAM -B -g $G -q $Q --keep-dup auto --nomodel --extsize $S -t ../mergedBams/$IP.bam -c ../mergedBams/$INPUT.bam -n $NAME 2>&1 | tee logs/$NAME.macs.log

deactivate