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setup.py
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setup.py
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#!/usr/bin/env python
from setuptools import setup, Extension
import glob
#install_requires=[ "pbcore >= 0.6.3", "networkx >= 1.7" ]
install_requires=[ "networkx >= 1.7" ]
scripts = glob.glob("src/py_scripts/*.py")
setup(name='falcon_kit',
version='0.4.0',
description='a small toolkit for DNA seqeucne alignment, overlapping, and assembly',
author='Jason Chin',
author_email='jchin@pacificbiosciences.com',
packages=['falcon_kit',
'falcon_kit.mains',
'falcon_kit.util',
],
package_dir={'falcon_kit':'src/py/'},
ext_modules=[
Extension('falcon_kit.ext_falcon', ['src/c/ext_falcon.c', 'src/c/DW_banded.c', 'src/c/kmer_lookup.c', 'src/c/falcon.c'],
extra_link_args=[],
extra_compile_args=['-fPIC', '-O3', '-fno-omit-frame-pointer'],
# '-fno-omit-frame-pointer' can help with gperftools.
#libraries=['profiler'],
#include_dirs=['/home/cdunn/local/include'],
#library_dirs=['/home/cdunn/local/lib'],
#language="c++", # c for now
#export_symbols=['generate_consensus'], # for windows?
),
],
entry_points = {'console_scripts': [
'falcon-task=falcon_kit.mains.tasks:main',
'fc_actg_coordinate=falcon_kit.mains.actg_coordinate:main',
'fc_consensus=falcon_kit.mains.consensus:main',
'fc_contig_annotate=falcon_kit.mains.contig_annotate:main',
'fc_ctg_link_analysis=falcon_kit.mains.ctg_link_analysis:main',
'fc_dedup_a_tigs=falcon_kit.mains.dedup_a_tigs:main',
'fc_graph_to_contig=falcon_kit.mains.graph_to_contig:main',
'fc_graph_to_utgs=falcon_kit.mains.graph_to_utgs:main',
'fc_ovlp_filter=falcon_kit.mains.ovlp_filter:main',
'fc_ovlp_stats=falcon_kit.mains.ovlp_stats:main',
'fc_ovlp_to_graph=falcon_kit.mains.ovlp_to_graph:main',
'fc_run=falcon_kit.mains.run:main',
],
},
extras_require = {
'falcon-task': ['falcon_kit'],
},
scripts = scripts,
zip_safe = False,
setup_requires=install_requires,
install_requires=install_requires
)