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setup.py
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setup.py
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from setuptools import setup, find_packages
from setuptools import Extension
import os
from io import open
from compile_externals import compile_all
import versioneer
CONFIG_NAME = "gimmemotifs.cfg"
DESCRIPTION = "GimmeMotifs is a motif prediction pipeline."
with open("README.md", encoding="utf-8") as f:
long_description = f.read().strip("\n")
# are we in the conda build environment?
conda_build = os.environ.get("CONDA_BUILD")
module1 = Extension("gimmemotifs.c_metrics", sources=["gimmemotifs/c_metrics.c"])
MOTIF_BINS = {
"MDmodule": ["src/MDmodule/MDmodule"],
"BioProspector": ["src/BioProspector/BioProspector"],
"Posmo": ["src/posmo/posmo", "src/posmo/clusterwd"],
"AMD": ["src/AMD/AMD.bin"],
}
cmdclass = versioneer.get_cmdclass()
my_build_py = cmdclass["build_py"]
class build_tools(my_build_py):
user_options = []
def initialize_options(self):
my_build_py.initialize_options(self)
self.build_base = None
self.build_lib = None
def finalize_options(self):
my_build_py.finalize_options(self)
self.set_undefined_options("build", ("build_base", "build_base"))
self.set_undefined_options("build", ("build_lib", "build_lib"))
def run(self):
if not self.dry_run:
src_dir = os.path.join(self.build_base, "src")
target_dir = os.path.join(self.build_lib, "gimmemotifs/included_tools")
# package_data={'gimmemotifs.data':['data/cfg/*']},
self.copy_tree("src/", src_dir)
# mkpath is a distutils helper to create directories
self.mkpath(target_dir)
compile_all(src_dir=src_dir)
for exes in MOTIF_BINS.values():
for exe in exes:
if os.path.exists(exe):
self.copy_file(exe, target_dir)
exe = os.path.join(self.build_base, exe)
if os.path.exists(exe):
self.copy_file(exe, target_dir)
self.copy_tree(
os.path.join(src_dir, "ChIPMunk"), os.path.join(target_dir, "ChIPMunk")
)
self.copy_tree(
os.path.join(src_dir, "HMS"), os.path.join(target_dir, "HMS")
)
self.copy_file(
os.path.join(src_dir, "MotifSampler/MotifSampler_x86_64"),
os.path.join(target_dir, "MotifSampler"),
)
self.copy_file(
os.path.join(src_dir, "MotifSampler/CreateBackgroundModel_x86_64"),
os.path.join(target_dir, "CreateBackgroundModel"),
)
self.copy_file(
os.path.join(src_dir, "Improbizer/ameme_x86_64"),
os.path.join(target_dir, "ameme"),
)
my_build_py.run(self)
cmdclass["build_py"] = build_tools
setup(
name="gimmemotifs",
version=versioneer.get_version(),
long_description=long_description,
long_description_content_type="text/markdown",
description=DESCRIPTION,
author="Simon van Heeringen",
author_email="[email protected]",
url="https://github.com/simonvh/gimmemotifs/",
download_url="https://github.com/simonvh/gimmemotifs/tarball/"
+ versioneer.get_version(),
license="MIT",
packages=find_packages(),
scripts=["scripts/gimme", "scripts/combine_peaks", "scripts/coverage_table"],
include_package_data=True,
ext_modules=[module1],
cmdclass=cmdclass,
classifiers=[
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: MacOS :: MacOS X",
"Operating System :: POSIX :: Linux",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3.5",
"Topic :: Scientific/Engineering :: Bio-Informatics",
],
install_requires=[
"setuptools >= 0.7",
"numpy",
"scipy >= 0.9.0",
"matplotlib >= 2",
"jinja2",
"pyyaml >= 3.10",
"pybedtools",
"statsmodels",
"scikit-learn",
"sklearn-contrib-lightning",
"seaborn",
"pysam",
"xgboost >= 0.71",
"xdg",
"diskcache",
"xxhash",
"configparser",
"six",
"future",
"genomepy",
"tqdm",
"pillow",
"logomaker",
],
)