#!/usr/bin/env python
#
# Wrapper script for invoking the jar.
#
# This script is written for use with the Conda package manager and is ported
# from a bash script that does the same thing, adapting the style in
# the peptide-shaker wrapper
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shaker.py)
import subprocess
import sys
import os
from os import access, getenv, path, X_OK
# Expected name of the VarScan JAR file.
JAR_NAME = 'womtool-85.jar'
PKG_NAME = 'womtool'
# Default options passed to the `java` executable.
# DEFAULT_JVM_MEM_OPTS = ['-Xms512m', '-Xmx1g']
DEFAULT_JVM_MEM_OPTS = []
def real_dirname(in_path):
"""Returns the path to the JAR file"""
realPath = os.path.dirname(os.path.realpath(in_path))
newPath = realPath
return newPath
def java_executable():
"""Returns the name of the Java executable."""
java_home = getenv('JAVA_HOME')
java_bin = path.join('bin', 'java')
env_prefix = os.path.dirname(os.path.dirname(real_dirname(sys.argv[0])))
if java_home and access(os.path.join(java_home, java_bin), X_OK):
return os.path.join(java_home, java_bin)
else:
# Use Java installed with Anaconda to ensure correct version
return os.path.join(env_prefix, 'bin', 'java')
def jvm_opts(argv, default_mem_opts=DEFAULT_JVM_MEM_OPTS):
"""Constructs a 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') or arg.startswith('-XX'):
opts_list = prop_opts
elif arg.startswith('-Xm'):
opts_list = mem_opts
else:
opts_list = pass_args
opts_list.append(arg)
if mem_opts == [] and getenv('_JAVA_OPTIONS') is None:
mem_opts = default_mem_opts
return (mem_opts, prop_opts, pass_args)
def main():
java = java_executable()
jar_dir = "/usr/local/lib"
(mem_opts, prop_opts, pass_args) = jvm_opts(sys.argv[1:])
if pass_args != [] and pass_args[0].startswith('org'):
jar_arg = '-cp'
else:
jar_arg = '-jar'
jar_path = path.join(jar_dir, JAR_NAME)
java_args = [java] + mem_opts + prop_opts + [jar_arg] + [jar_path] + pass_args
sys.exit(subprocess.call(java_args))
if __name__ == "__main__":
main()
