#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -M cecilia.klein@crg.es 
#$ -q rg-el7
#$ -l h_rt=6:0:00
#$ -m a 
#$ -V 
#$ -N cmnd.bw
#$ -l virtual_free=12G 
#$ -pe smp 1
#$ -e /nfs/users2/rg/cklein/dmel/silvia_et_al_2015/cluster.bw/cmnd.bw.$TASK_ID.ERR
#$ -o /nfs/users2/rg/cklein/dmel/silvia_et_al_2015/cluster.bw/cmnd.bw.$TASK_ID.LOG
#$ -t 1-20
export PATH=~/bin:$PATH
awk -v task_id=$SGE_TASK_ID -F"#" 'BEGIN{pat="^#" task_id "# "}$0 ~ pat{gsub(/^\s+/,"",$3);print $3 | "/bin/bash -l"}' /nfs/users2/rg/cklein/dmel/silvia_et_al_2015/cluster.bw/cmnd.bw
#1# zcat GSM1060711_H3_wing.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1060711_H3_wing.aligned.bw
#2# zcat GSM1060712_H3_eye.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1060712_H3_eye.aligned.bw
#3# zcat GSM1060713_H3K36me3_eye.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1060713_H3K36me3_eye.aligned.bw
#4# zcat GSM1060714_H3K4me3_eye.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1060714_H3K4me3_eye.aligned.bw
#5# zcat GSM1060715_WING_RNASEQ.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1060715_WING_RNASEQ.aligned.bw
#6# zcat GSM1060716_EYE_RNASEQ.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1060716_EYE_RNASEQ.aligned.bw
#7# zcat GSM1182471_H3K4me1_WID_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1182471_H3K4me1_WID_R1.bw
#8# zcat GSM1182472_H3K27ac_WID_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1182472_H3K27ac_WID_R1.bw
#9# zcat GSM1182473_H3K4me1_EID_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1182473_H3K4me1_EID_R1.bw
#10# zcat GSM1182474_H3K27ac_EID_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1182474_H3K27ac_EID_R1.bw
#11# zcat GSM1363588_EID_H3K27me3_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1363588_EID_H3K27me3_R1.bw
#12# zcat GSM1363589_EID_H3K9ac_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1363589_EID_H3K9ac_R1.bw
#13# zcat GSM1363590_WID_H3K9ac_R1.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM1363590_WID_H3K9ac_R1.bw
#14# zcat GSM593407_Ash2.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593407_Ash2.aligned.bw
#15# zcat GSM593408_H3K4me3.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593408_H3K4me3.aligned.bw
#16# zcat GSM593409_H3K27me3.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593409_H3K27me3.aligned.bw
#17# zcat GSM593410_H3K36me3.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593410_H3K36me3.aligned.bw
#18# zcat GSM593411_Pol2Ser2P.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593411_Pol2Ser2P.aligned.bw
#19# zcat GSM593412_Pol2Ser5P.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593412_Pol2Ser5P.aligned.bw
#20# zcat GSM593413_Input.aligned.wig.gz| grep -vP "^track" | grep -vP ^0| ~cklein/bin/kentUtils/bin/linux.x86_64/wigToBigWig -clip stdin dm3.fa.fai GSM593413_Input.aligned.bw