set a makefile as pipeline

CONFIG

BAM=your.bam
OUT=your.out

makefile

#!/usr/bin/env make -

HOME=/Users/zhuxp/Projects/lnc
GENOME=/Users/zhuxp/Data/genome/mm9.2bit
BAM=$(HOME)/BL6RNASeq/long250.miseq.gsnap.sorted.bam
PID=test007
INPUT=$(HOME)/tmp.bed
all: $(PID).out
$(PID).splicesites.bed: $(BAM)
	xBamToSpliceSites.py -i $(BAM) -o $@ -s read2 -g $(GENOME)
$(PID).splicesites.sorted.bed: $(PID).splicesites.bed
	bedSort $^ $@

$(PID).splicesites.sorted.bed.gz: $(PID).splicesites.sorted.bed
	bgzip -c $^ > $@


$(PID).splicesites.sorted.bed.gz.tbi: $(PID).splicesites.sorted.bed.gz
	tabix $^


$(PID).out: $(PID).splicesites.sorted.bed.gz.tbi
	xBam8.py -s $(PID).splicesites.sorted.bed.gz -i $(INPUT) -b $(BAM) -o $(PID).out

clean:
	rm $(PID).*

makefile2

#!/usr/bin/env make -

HOME=/Users/zhuxp/Projects/lnc
GENOME=/Users/zhuxp/Data/genome/mm9.2bit
BAM=$(HOME)/BL6RNASeq/long250.miseq.gsnap.bam
PID=test007
INPUT=$(HOME)/tmp.bed
all: $(PID).out
include CONFIG
$(PID).splicesites.bed: $(BAM)
	xBamToSpliceSites.py -i $(BAM) -o $@ -s read2 -g $(GENOME)
$(PID).splicesites.bed.gz: $(PID).splicesites.bed
	bedSort $^ $^
	bgzip $^
	tabix $@
$(PID).out: $(PID).splicesites.bed.gz 
	xBam8.py -s $(PID).splicesites.bed.gz -i $(INPUT) -b $(BAM) -o $(PID).out
clean:
	rm $(PID).*
test: 
	echo $(basename $(PID))
	echo $(INPUT)
	echo $(BAM)

read_config.py

#!/usr/bin/env python
# Programmer : zhuxp
# Date: 
# Last-modified: 12-10-2013, 16:26:18 EST
VERSION="0.1"
import os,sys,argparse
from xplib.Tools import IO

def ParseArg():
    ''' This Function Parse the Argument '''
    p=argparse.ArgumentParser( description = 'Example: %(prog)s -h', epilog='Library dependency : xplib')
    p.add_argument('-v','--version',action='version',version='%(prog)s '+VERSION)
    p.add_argument('-i','--input',dest="input",default="stdin",type=str,help="input file DEFAULT: STDIN")
    
    if len(sys.argv)==1:
        print >>sys.stderr,p.print_help()
        exit(0)
    return p.parse_args()
def Main():
    '''
    IO TEMPLATE
    '''
    global args,out
    args=ParseArg()
    fin=IO.fopen(args.input,"r")
    config=IO.read_config(fin)
    print config






    
if __name__=="__main__":
    Main()