#!/usr/bin/env python
from setuptools import setup
import versionpy
import hpc_utils
pkg = hpc_utils.__name__
version = versionpy.get_version(pkg)
setup(
name=pkg,
version=version,
author='Vlad Saveliev',
author_email='*****@*****.**',
description=
'Cluster utils and paths to the reference data in UMCCR servers',
keywords='bioinformatics',
url='https://github.com/umccr/' + pkg,
license='GPLv3',
packages=[
pkg,
],
package_data={
pkg: versionpy.find_package_files('', pkg),
},
include_package_data=True,
zip_safe=False,
install_requires=versionpy.get_reqs(),
)
from setuptools import setup
pkg = 'ngs_utils'
try:
import versionpy
except ImportError:
res = input('Installation requires versionpy. Install it now? [Y/n]')
if res.lower().startswith('n'):
raise
os.system('pip install versionpy')
import versionpy
version = versionpy.get_version(pkg)
package_data = {
pkg: versionpy.find_package_files('', pkg, skip_exts=['.sass', '.coffee'])
}
setup(
name=pkg,
version=version,
author='Vlad Savelyev',
author_email='*****@*****.**',
description='Python utilities for bioinformatics tools and pipelines',
long_description=open('README.md').read(),
url='https://github.com/vladsaveliev/NGS_Utils',
license='GPLv3',
packages=[pkg],
package_data=package_data,
include_package_data=True,
zip_safe=False,
version = versionpy.get_version(package_name)
setup(
name=package_name,
version=version,
author='Vlad Saveliev',
author_email='*****@*****.**',
description='Utils for NGS pipelines by Vlad Saveliev',
keywords='bioinformatics',
url='https://github.com/vladsaveliev/NGS_Utils',
license='GPLv3',
packages=[
package_name,
],
package_data={
package_name: versionpy.find_package_files('', package_name, skip_exts=['.sass', '.coffee'])
},
include_package_data=True,
zip_safe=False,
install_requires=versionpy.get_reqs(),
setup_requires=['numpy'],
scripts=[path for path in
[join('scripts', fn) for fn in [
'standardize_bed.py',
'split_bed.py',
'qstat.py',
'sort_bed.py',
'bed_file_from_gene_list.py',
'html_to_base64.py',
'group_and_merge_by_gene.py',
'hg19_addchr.py',
import os
from setuptools import setup
pkg = 'test_ci'
try:
import versionpy
except ImportError:
res = input('Installation requires versionpy. Install it now? [Y/n]')
if res.lower().startswith('n'):
raise
os.system('pip install versionpy')
import versionpy
version = versionpy.get_version(pkg)
package_data = {pkg: versionpy.find_package_files('', pkg)}
setup(
name=pkg,
script_name=pkg,
version=version,
author='Vlad Savelyev',
author_email='*****@*****.**',
description='Toy repo to test CI',
long_description=(open('README.md').read()),
long_description_content_type="text/markdown",
url=f'https://github.com/vladsaveliev/{pkg}',
license='GPLv3',
packages=[pkg],
package_data=package_data,
include_package_data=True,
pkg = 'umccrise'
version = get_version(pkg)
setup(
name='umccrise',
version=version,
author='Vlad Saveliev',
author_email='*****@*****.**',
description='UMCCRisation of bcbio-nextgen analysis results',
keywords='bioinformatics',
url='https://github.com/umccr/umccrise',
license='GPLv3',
package_data={
pkg: find_package_files('', pkg),
},
packages=find_packages(),
scripts=[
'vendor/vcfToBedpe',
'scripts/umccrise',
'scripts/pcgr',
'scripts/conpair',
'scripts/gpl.py',
'scripts/gridss.py',
'scripts/umccrise_refdata_pull',
],
include_package_data=True,
zip_safe=False,
# For MultiQC_umccr
entry_points={