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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015-2019 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", "executors", "scripts"]
# 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 isfile(os.path.join(spades_home, "spades-core")):
install_prefix = dirname(spades_home)
bin_home = '/usr/libexec/spades'
spades_home = '/usr/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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