pb_assembly/FALCON/setup.py

#!/usr/bin/env python3.7

from setuptools import setup, Extension


# requires.txt
# networkx>=1.9.1
# python-edlib
# python-msgpack
# future>=0.16.0
# pypeFLOW>=2.0.0
install_requires = [
    "networkx >=1.9.1",
    # "python-edlib",
    # "python-msgpack",
    # "pb-dazzler",
    "future >= 0.16.0",
    #"pypeFLOW >= 2.0.0",

]

# https://docs.python.org/3/extending/building.html
# module1 = Extension('demo',
#                     define_macros = [('MAJOR_VERSION', '1'),
#                                      ('MINOR_VERSION', '0')],
#                     include_dirs = ['/usr/local/include'],
#                     libraries = ['tcl83'],
#                     library_dirs = ['/usr/local/lib'],
#                     sources = ['demo.c'])
ext_falcon_module = Extension(
    'ext_falcon',
    sources=['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'],
    # library_dirs=['/home/cdunn/local/lib'],
    # language="c++", # c for now
    # export_symbols=['generate_consensus'], # for windows?
)

scripts = []

# PKG-INFO
# Metadata-Version: 2.1
# Name: falcon-kit
# Version: 1.4.2
# Summary: a small toolkit for DNA seqeucne alignment, overlapping, and assembly
# Home-page: UNKNOWN
# Author: Jason Chin
# Author-email: jchin@pacificbiosciences.com
# License: UNKNOWN
# Description: UNKNOWN
# Platform: UNKNOWN
# Provides-Extra: falcon-task
setup(name='falcon_kit',
      version='1.4.2',
      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': 'falcon_kit/'},
      ext_modules=[ext_falcon_module],
      entry_points={'console_scripts': [
            'falcon-task = falcon_kit.mains.tasks:main',
            'fc_actg_coordinate = falcon_kit.mains.actg_coordinate:main',
            'fc_calc_cutoff = falcon_kit.mains.calc_cutoff: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_fasta2fasta = falcon_kit.mains.fasta2fasta:main',
            'fc_fetch_reads = falcon_kit.mains.fetch_reads:main',
            'fc_gen_gfa_v1 = falcon_kit.mains.gen_gfa_v1:main',
            'fc_get_read_ctg_map = falcon_kit.mains.get_read_ctg_map: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_pr_ctg_track = falcon_kit.mains.pr_ctg_track:main',
            'fc_rr_ctg_track = falcon_kit.mains.rr_ctg_track:main',
            'fc_run = falcon_kit.mains.run1:main',
            'fc_run.py = falcon_kit.mains.run1:main',
            'fc_run1 = falcon_kit.mains.run1:main',
        ],
      },
      extras_require={
          'falcon-task':  ['falcon_kit'],
      },
      scripts=scripts,
      zip_safe=False,
      install_requires=install_requires,
)