new_contents: #!/usr/bin/env python
  #
  # Wrapper script for Java Conda packages that ensures that the java runtime
  # is invoked with the right options. Adapted from the bash script (http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128).
  #
  
  #
  # Program Parameters
  #
  import os
  import sys
  import subprocess
  from os import access, getenv, X_OK
  jar_file = 'MSGFPlus.jar'
  
  default_jvm_mem_opts = ['-Xms512m', '-Xmx1g']
  
  # !!! End of parameter section. No user-serviceable code below this line !!!
  
  def real_dirname(path):
      """Return the symlink-resolved, canonicalized directory-portion of path."""
      return os.path.dirname(os.path.realpath(path))
  
  
  def java_executable():
      """Return the executable name of the Java interpreter."""
      java_home = getenv('JAVA_HOME')
      java_bin = os.path.join('bin', 'java')
  
      if java_home and access(os.path.join(java_home, java_bin), X_OK):
          return os.path.join(java_home, java_bin)
      else:
          return 'java'
  
  
  def jvm_opts(argv):
      """Construct list of Java arguments based on our argument list.
  
      The argument list passed in argv must not include the script name.
      The return value is a 3-tuple lists of strings of the form:
        (memory_options, prop_options, passthrough_options)
      """
      mem_opts = []
      prop_opts = []
      pass_args = []
  
      for arg in argv:
          if arg.startswith('-D'):
              prop_opts.append(arg)
          elif arg.startswith('-XX'):
              prop_opts.append(arg)
          elif arg.startswith('-Xm'):
              mem_opts.append(arg)
          else:
              pass_args.append(arg)
  
      # In the original shell script the test coded below read:
      #   if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]
      # To reproduce the behaviour of the above shell code fragment
      # it is important to explictly check for equality with None
      # in the second condition, so a null envar value counts as True!
  
      if mem_opts == [] and getenv('_JAVA_OPTIONS') == None:
          mem_opts = default_jvm_mem_opts
  
      return (mem_opts, prop_opts, pass_args)
  
  
  def main():
      java = java_executable()
      jar_dir = real_dirname(sys.argv[0])
      (mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:])
  
      if pass_args != [] and pass_args[0].startswith('eu'):
          jar_arg = '-cp'
      else:
          jar_arg = '-jar'
  
      jar_path = os.path.join(jar_dir, jar_file)
  
      java_args = [java]+ mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args
  
      sys.exit(subprocess.call(java_args))
  
  
  if __name__ == '__main__':
      main()
  
subject: Add script to launch ms-gf