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#(c) 2016-2019 by Authors
#This file is a part of the Flye package
#Released under the BSD license (see LICENSE file)
from __future__ import print_function
import os
import sys
import subprocess
import shutil
try:
import setuptools
except ImportError:
sys.exit("setuptools package not found. "
"Please use 'pip install setuptools' first")
from setuptools import setup
from setuptools.command.install import install as SetuptoolsInstall
from distutils.command.build import build as DistutilsBuild
from distutils.spawn import find_executable
# Make sure we're running from the setup.py directory.
script_dir = os.path.dirname(os.path.realpath(__file__))
if script_dir != os.getcwd():
os.chdir(script_dir)
from flye.__version__ import __version__
class MakeBuild(DistutilsBuild):
def run(self):
DistutilsBuild.run(self)
if not find_executable("make"):
sys.exit("ERROR: 'make' command is unavailable")
try:
subprocess.check_call(["make"])
except subprocess.CalledProcessError as e:
sys.exit("Compilation error: ", e)
class MakeInstall(SetuptoolsInstall):
def run(self):
SetuptoolsInstall.run(self)
print('Installing C++ binaries')
if os.path.isdir(self.install_lib) and not os.access(self.install_lib, os.W_OK):
sys.exit('Error: no write permission for ' + self.install_lib + ' ' +
'Perhaps you need to use sudo?')
if os.path.isdir(self.install_scripts) and not os.access(self.install_scripts, os.W_OK):
sys.exit('Error: no write permission for ' + self.install_scripts + ' ' +
'Perhaps you need to use sudo?')
if not os.path.exists(self.install_scripts):
os.makedirs(self.install_scripts)
build_dir = os.path.join(script_dir, "bin")
install_dir = self.install_scripts
bin_files = ['flye-modules']
for file in bin_files:
if not os.path.isfile(os.path.join(build_dir, file)):
sys.exit('Error: binary not found: ' + file)
shutil.copy2(os.path.join(build_dir, file),
os.path.join(install_dir, file))
setup(name='flye',
version=__version__,
description='De novo assembler for single molecule sequencing reads using repeat graphs',
url='https://github.com/fenderglass/Flye',
author='Mikhail Kolmogorov',
author_email = 'fenderglass@gmail.com',
license='BSD-3-Clause',
packages=['flye', 'flye/assembly', 'flye/config', 'flye/polishing',
'flye/utils', 'flye/repeat_graph', 'flye/short_plasmids',
'flye/trestle', 'flye/tests'],
package_data={'flye': ['config/bin_cfg/*', 'tests/data/*']},
entry_points={'console_scripts': ['flye = flye.main:main']},
cmdclass={'build': MakeBuild,
'install' : MakeInstall}
)
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