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#!/usr/bin/env python
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import os
import sys
from os.path import abspath, dirname, realpath, join, isfile
source_dirs = ["", "truspades", "common"]
# developers configuration
spades_home = abspath(dirname(realpath(__file__)))
bin_home = join(spades_home, 'bin')
python_modules_home = join(spades_home, 'src')
ext_python_modules_home = join(spades_home, 'ext', 'src', 'python_libs')
spades_version = ''
def init():
global spades_home
global bin_home
global python_modules_home
global spades_version
global ext_python_modules_home
# users configuration (spades_init.py and spades binary are in the same directory)
if os.path.isfile('/usr/lib/spades/bin/spades'):
bin_home = '/usr/lib/spades/bin/'
spades_home = '/usr/share/spades'
python_modules_home = spades_home
ext_python_modules_home = spades_home
elif os.path.isfile(os.path.join(spades_home, 'spades')):
install_prefix = dirname(spades_home)
bin_home = join(install_prefix, 'bin')
spades_home = join(install_prefix, 'share', 'spades')
python_modules_home = spades_home
ext_python_modules_home = spades_home
for dir in source_dirs:
sys.path.append(join(python_modules_home, 'spades_pipeline', dir))
spades_version = open(join(spades_home, 'VERSION'), 'r').readline().strip()
if __name__ == '__main__':
spades_py_path = join(dirname(realpath(__file__)), 'spades.py')
sys.stderr.write('Please use ' + spades_py_path + ' for running SPAdes genome assembler\n')
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