old_contents: #!/usr/bin/env python
  import os
  import sys
  major=sys.version_info[0]
  
  errors=[]
  
  def error(msg):
  	errors.append(msg)
  
  def sub(cmd):
  	if os.system(cmd) != 0:
  		errors.append("Command failed: %s"%cmd)
  
  print("Checking Python version...")
  if major != 2:
  	error("Teaser currently requires Python 2! Version: %s"%str(sys.version_info))
  
  print("Installing Python package dependencies...")
  sub("pip install --user intervaltree tornado pyaml psutil")
  
  print("Downloading software packages (Mappers and Simulators)...")
  sub("wget http://www.cibiv.at/software/teaser/teaser_software.tar.gz")
  sub("tar -xvzf teaser_software.tar.gz")
  
  print("Downloading example reference genome (E. coli)...")
  os.chdir("references")
  sub("wget http://www.cibiv.at/software/teaser/E_coli.fasta")
  os.chdir("..")
  
  print("Building BWA...")
  os.chdir("software/bwa_build")
  sub("make")
  os.chdir("..")
  sub("mv bwa bwa_prebuilt")
  sub("cp bwa_build/bwa bwa")
  os.chdir("..")
  
  print("Building NGM...")
  os.chdir("software/ngm_build")
  sub("mkdir -p build/release")
  os.chdir("build/release")
  sub("cmake -DCMAKE_BUILD_TYPE=Release ../..")
  sub("make")
  os.chdir("../../../")
  sub("cp -R ngm_build/bin/ngm-0.4.13/* ngm")
  os.chdir("..")
  
  print("Building DWGSIM...")
  os.chdir("software/dwgsim_build")
  sub("make")
  os.chdir("..")
  sub("mv dwgsim dwgsim_prebuilt")
  sub("cp dwgsim_build/dwgsim dwgsim")
  os.chdir("..")
  
  sub("rm teaser_software.tar.gz")
  
  if len(errors)==0:
  	print("Installation completed successfully!")
  else:
  	print("Errors occured during installation:")
  	for msg in errors:
  		print("\t%s"%msg)
  
new_contents: #!/usr/bin/env python
  import os
  import sys
  major=sys.version_info[0]
  
  errors=[]
  
  def error(msg):
  	errors.append(msg)
  
  def sub(cmd):
  	if os.system(cmd) != 0:
  		errors.append("Command failed: %s"%cmd)
  		return False
  	else:
  		return True
  
  print("Checking Python version...")
  if major != 2:
  	error("Teaser currently requires Python 2! Version: %s"%str(sys.version_info))
  
  print("Installing Python package dependencies...")
  sub("pip install --user intervaltree tornado pyaml psutil")
  
  print("Downloading software packages (Mappers and Simulators)...")
  sub("wget http://www.cibiv.at/software/teaser/teaser_software.tar.gz")
  sub("tar -xvzf teaser_software.tar.gz")
  
  print("Downloading example reference genome (E. coli)...")
  os.chdir("references")
  sub("wget http://www.cibiv.at/software/teaser/E_coli.fasta")
  os.chdir("..")
  
  print("Building BWA...")
  os.chdir("software/bwa_build")
  bwa_build_success=sub("make")
  os.chdir("..")
  if bwa_build_success:
  	sub("mv bwa bwa_prebuilt")
  	sub("cp bwa_build/bwa bwa")
  os.chdir("..")
  
  print("Building NGM...")
  os.chdir("software/ngm_build")
  sub("mkdir -p build/release")
  os.chdir("build/release")
  sub("cmake -DCMAKE_BUILD_TYPE=Release ../..")
  sub("make")
  os.chdir("../../../")
  sub("cp -R ngm_build/bin/ngm-0.4.13/* ngm")
  os.chdir("..")
  
  print("Building DWGSIM...")
  os.chdir("software/dwgsim_build")
  dwgsim_build_success=sub("make")
  os.chdir("..")
  if dwgsim_build_success:
  	sub("mv dwgsim dwgsim_prebuilt")
  	sub("cp dwgsim_build/dwgsim dwgsim")
  os.chdir("..")
  
  sub("rm teaser_software.tar.gz")
  
  if len(errors)==0:
  	print("Installation completed successfully!")
  else:
  	print("Errors occured during installation:")
  	for msg in errors:
  		print("\t%s"%msg)
  
subject: Install script update