configure

#!/usr/bin/env python
import argparse
author='Julien Fouret'
contact='julien@fouret.me'

parser = argparse.ArgumentParser(description='Configure makefile for installation',epilog="Author : "+author+" for more informations or enquiries please contact "+contact,formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-bin_path', metavar='', required=False,default="/usr/bin/", help="a bin directory present in env $PATH to call executables")
parser.add_argument('-lib_path', metavar='', required=False,default="/usr/lib/", help="a lib directory present in env $LD_LIBRARY_PATH to call executables")
parser.add_argument('-picard', metavar='', required=False,default="/export/bin/picard-tools-2.1.0/picard.jar", help="path of picardtools jar file")
parser.add_argument('-macse', metavar='', required=False,default="/export/source/script/macse_v1.2.jar", help="path of macse jar file")
parser.add_argument('-queue', metavar='', required=False,default="all", help="default queue to use for HPC")

args=parser.parse_args()

import os
with open('makefile','w') as mf:
	mf.write("# CAN BE CHANGED\n\n")
	mf.write("BINPATH="+os.path.abspath(args.bin_path)+"\n")
	mf.write("LIBPATH="+os.path.abspath(args.lib_path)+"\n")
	mf.write("PICARD="+os.path.abspath(args.picard)+"\n")
	mf.write("MACSE="+os.path.abspath(args.macse)+"\n")
	mf.write("QUEUE="+args.queue+"\n\n")
	mfin=open("makefile.in")
	mf.write(mfin.read())
	mfin.close()