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import os
import shutil
import sys
import glob
from setuptools import setup, find_packages, Extension
#minimap_c_files = [
# 'bseq.c',
# 'index.c',
# 'kthread.c',
# 'map.c',
# 'misc.c',
# 'sdust.c',
# 'sketch.c',
#]
#minimap_c_files = [os.path.join('third_party', 'minimap-0.2', x) for x in minimap_c_files]
minimap_c_files = [os.path.join('ariba', 'ext', 'minimap_ariba.cpp')]
minimap_mod = Extension(
"minimap_ariba",
minimap_c_files,
extra_link_args=['-lz', '-lminimap'],
include_dirs=[os.path.join(os.path.sep, 'usr', 'include', 'minimap')],
)
#fermilite_c_files = [
# 'bfc.c',
# 'bseq.c',
# 'bubble.c',
# 'htab.c',
# 'ksw.c',
# 'kthread.c',
# 'mag.c',
# 'misc.c',
# 'mrope.c',
# 'rld0.c',
# 'rle.c',
# 'rope.c',
# 'unitig.c'
#]
#fermilite_c_files = [os.path.join('third_party', 'fermi-lite-0.1', x) for x in fermilite_c_files]
fermilite_c_files = [os.path.join('ariba', 'ext', 'fml-asm_ariba.cpp')]
fermilite_mod = Extension(
"fermilite_ariba",
fermilite_c_files,
extra_link_args=['-lz', '-lfml'],
#include_dirs=[os.path.join('third_party', 'fermi-lite-0.1')],
)
vcfcall_mod = Extension(
"vcfcall_ariba",
[os.path.join('ariba', 'ext', 'vcfcall_ariba.cpp')],
)
setup(
ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
name='ariba',
version='2.6.1',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
author='Martin Hunt',
author_email='path-help@sanger.ac.uk',
url='https://github.com/sanger-pathogens/ariba',
scripts=glob.glob('scripts/*'),
test_suite='nose.collector',
tests_require=['nose >= 1.3'],
install_requires=[
'dendropy >= 4.1.0',
'pyfastaq >= 3.12.0',
'pysam >= 0.9.1',
'pymummer>=0.10.1',
],
license='GPLv3',
classifiers=[
'Development Status :: 4 - Beta',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Programming Language :: Python :: 3 :: Only',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
],
)
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