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setup.py
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# -*- coding: utf-8 -*-
# License: 3-clause BSD
__revision__ = "$Id: $" # for the SVN Id
import sys
import os
from setuptools import setup, find_packages
import glob
_MAJOR = 0
_MINOR = 9
_MICRO = 1
version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
release = '%d.%d' % (_MAJOR, _MINOR)
metainfo = {
'authors': {"main": ("Thomas Cokelaer", "thomas.cokelaer@pasteur.fr")},
'maintainer': {"main": ("Thomas Cokelaer", "thomas.cokelaer@pasteur.fr")},
'version': version,
'license' : 'new BSD',
'download_url': "/~https://github.com/sequana/sequana/archive/{0}.tar.gz".format(version),
'url' : "http://github.com/sequana/sequana",
'description': "A set of standalone application and pipelines dedicated to NGS (new generation sequencing) analysis" ,
'platforms' : ['Linux', 'Unix', 'MacOsX', 'Windows'],
'keywords' : ['NGS', 'snakemake'],
'classifiers' : [
'Development Status :: 5 - Production/Stable',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Operating System :: OS Independent',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Topic :: Software Development :: Libraries :: Python Modules',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Information Analysis',
'Topic :: Scientific/Engineering :: Mathematics',
'Topic :: Scientific/Engineering :: Physics']
}
packages = find_packages()
packages = [this for this in packages if this.startswith('test.') is False]
packages = [this for this in packages if this not in ['test']]
# load a common list of requirements
# - mock is for the test only
# - qtconsole is required by Sequanix
requirements = open("requirements.txt").read().split()
# not in conda but on pypi
requirements += ["itolapi"]
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
if on_rtd:
# pillow, sphinx, numpydoc are for the doc only
extra_packages = ["pillow", "numpydoc", "sphinx"]
requirements += extra_packages
if sys.version_info.major == 2 or on_rtd:
requirements = [x for x in requirements
if x.startswith("snakemake") is False]
setup(
name = "sequana",
version = version,
maintainer = metainfo['authors']['main'][0],
maintainer_email = metainfo['authors']['main'][1],
author = metainfo['authors']['main'][0],
author_email = metainfo['authors']['main'][1],
long_description = open("README.rst").read(),
keywords = metainfo['keywords'],
description = metainfo['description'],
license = metainfo['license'],
platforms = metainfo['platforms'],
url = metainfo['url'],
download_url = metainfo['download_url'],
classifiers = metainfo['classifiers'],
# package installation
packages = packages,
# pillow, sphinx-gallery and numpydoc are for the doc only
# mock is for the test only qtconsole is required by Sequanix
install_requires = requirements,
# specific packages for testing
tests_require = open('requirements_dev.txt').read().split(),
# here below '': pattern means include that pattern in all packages
# so '' :['README.rst'] will include all README.rst recursively
# required to use python setup.py install
# This is recursive include of data files
exclude_package_data = {"": ["__pycache__"]},
package_data = {
'': ['Snakefile*', '*html', 'README.rst', "requirements*txt",
'config*.yaml', '*.css', "*.js",
"snpEff.config*", "*.fa", "*.rules"],
'sequana.rules' : ['*/*.rules', "*/*/*.rules", "*/*/*/*.rules"],
'sequana.pipelines' : ['*/*'],
'sequana.resources.data' : ['*.*'], # use *.* for files and not ./adapters
'sequana.resources.data.adapters' : ['*'],
'sequana.resources.images' : ['*'],
'sequana.resources.testing' : ['*'],
'sequana.resources.testing.rnadiff' : ['*/tables/*'],
'sequana.resources.busco' : ['*'],
'sequana.multiqc' : ['*yaml'],
},
# these files do not need to be added in MANIFEST.in since there are python
# packages that will be copied from sequana/ into sequana/
# Note, however, that e.g. ./pipelines must be added
zip_safe=False,
entry_points = {
'console_scripts':[
'sequanix=sequana.gui.sequana_gui:main',
#'fastq_head=sequana.scripts.fastq_head:main',
#'fastq_count=sequana.scripts.fastq_count:main',
'sequana_lane_merging=sequana.scripts.lane_merging:main',
'sequana=sequana.scripts.main:main',
'sequana_taxonomy=sequana.scripts.taxonomy:main',
'sequana_coverage=sequana.scripts.coverage:main',
'sequana_summary=sequana.scripts.summary:main',
'sequana_mapping=sequana.scripts.mapping:main',
'sequana_compressor=sequana.scripts.compressor:main',
'sequana_report=sequana.scripts.reports:main',
'sequana_vcf_filter=sequana.scripts.vcf_filter:main', # june 2018
'sequana_bam_splitter=sequana.scripts.bam_splitter:main', # aug 2018
'sequana_substractor=sequana.scripts.substractor:main', # march 2019
'sequana_start_pipeline=sequana.scripts.start_pipeline:main', # dec 2019
'sequana_gtf_fixer=sequana.scripts.gtf_fixer:main' # jan 2019
],
'sequana.module':[
'sequana_coverage=sequana.modules_report.coverage:CoverageModule',
'sequana_variant_calling=sequana.modules_report.variant_calling:VariantCallingModule',
'sequana_summary=sequana.modules_report.summary:SummaryModule',
],
"multiqc.modules.v1": [
"sequana_pacbio_qc=sequana.multiqc.pacbio_qc:MultiqcModule",
"sequana_quality_control=sequana.multiqc.quality_control:MultiqcModule",
"sequana_coverage=sequana.multiqc.coverage:MultiqcModule",
"sequana_isoseq=sequana.multiqc.isoseq:MultiqcModule",
"sequana_isoseq_qc=sequana.multiqc.isoseq_qc:MultiqcModule",
"sequana_bamtools_stats=sequana.multiqc.bamtools_stats:MultiqcModule",
"sequana_kraken=sequana.multiqc.kraken:MultiqcModule",
"sequana_pacbio_amplicon=sequana.multiqc.pacbio_amplicon:MultiqcModule"
],
'multiqc.hooks.v1': [
'before_config = sequana.multiqc.config:load_config',
]
},
)