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from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext
import os
import subprocess
import sys
__version__ = "2.2"
ROOT_DIR = os.getcwd()
SUBMOD_DIR = os.path.join(ROOT_DIR, "submods")
SUBMODS = [
]
class get_pybind_include(object):
"""Helper class to determine the pybind11 include path
The purpose of this class is to postpone importing pybind11
until it is actually installed, so that the ``get_include()``
method can be invoked. """
def __str__(self):
import pybind11
return pybind11.get_include()
class pre_build(build_ext):
def run(self):
submods_loaded = True
for submod in SUBMODS:
if not os.path.exists(os.path.join(SUBMOD_DIR, submod)):
submods_loaded = False
break
if not submods_loaded:
sys.stderr.write("Downloading submodules\n")
subprocess.check_call([
"git", "submodule", "update", "--init"
])
else:
sys.stderr.write("All submodules present\n")
if os.path.exists("/usr/lib/libbwa.a"):
sys.stderr.write("Found libbwa.a\n")
else:
sys.stderr.write("building libbwa\n")
subprocess.check_call([
"make",
"-C", "./submods/bwa",
"-f", "../../src/Makefile_bwa"
])
if True: # os.path.exists("./submods/hdf5/lib/libhdf5.a"):
sys.stderr.write("Found libhdf5.a\n")
else:
hdf5_dir = os.path.join(ROOT_DIR, "submods/hdf5")
os.chdir(hdf5_dir)
subprocess.check_call([
"./configure",
"--enable-threadsafe",
"--disable-hl",
"--prefix", hdf5_dir,
"--enable-shared=no",
"--with-pic=yes"
])
subprocess.check_call(["make"])
subprocess.check_call(["make", "install"])
os.chdir(ROOT_DIR)
build_ext.run(self)
uncalled = Extension(
"_uncalled",
sources = [
"src/event_profiler.cpp",
"src/pybinder.cpp",
"src/client_sim.cpp",
"src/fast5_reader.cpp",
"src/mapper.cpp",
"src/self_align_ref.cpp",
"src/map_pool.cpp",
"src/event_detector.cpp",
"src/read_buffer.cpp",
"src/chunk.cpp",
"src/realtime_pool.cpp",
"src/seed_tracker.cpp",
"src/normalizer.cpp",
"src/range.cpp"
],
include_dirs = [
"./submods", #TODO: consistent incl paths?
subprocess.check_output("pkg-config --cflags hdf5-serial | sed 's/-I//'", shell=True, encoding='UTF-8').strip(),
"/usr/include/fast5/",
"/usr/include/",
get_pybind_include()
],
library_dirs = [
"./submods/bwa",
subprocess.check_output("pkg-config --libs-only-L hdf5-serial | sed 's/-L//'", shell=True, encoding='UTF-8').strip()
],
libraries = ["bwa", "hdf5", "z", "dl", "m"],
extra_compile_args = ["-std=c++11", "-O3"],
define_macros = [("PYBIND", None)]
)
setup(
name = "uncalled",
version = __version__,
description = "Rapidly maps raw nanopore signal to DNA references",
author = "Sam Kovaka",
author_email = "skovaka@gmail.com",
url = "https://github.com/skovaka/UNCALLED",
classifiers=[
"Programming Language :: Python :: 3"
],
python_requires=">=3.6",
setup_requires=[
'pybind11>=2.5.0',
],
packages=find_packages(),
include_package_data=True,
scripts = ['scripts/uncalled'],
ext_modules = [uncalled],
cmdclass={'build_ext': pre_build},
)
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