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# Copyright (c) 2014-2016 Genome Research Ltd.
#
# This file is part of IVA.
#
# IVA is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 3 of the License, or (at your option) any later
# version.
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import glob
import sys
import shutil
from setuptools import setup, find_packages
required_progs = [
'kmc',
'kmc_dump',
'nucmer',
'delta-filter',
'show-coords',
'samtools',
'smalt'
]
found_all_progs = True
print('Checking dependencies found in path:')
for program in required_progs:
if shutil.which(program) is None:
found_all_progs = False
found = ' NOT FOUND'
else:
found = ' OK'
print(found, program, sep='\t')
if not found_all_progs:
print('Cannot install because some dependencies not found.', file=sys.stderr)
sys.exit(1)
setup(
name='iva',
version='1.0.9',
description='Iterative Virus Assembler',
packages = find_packages(),
package_data={'iva': ['gage/*', 'ratt/*', 'read_trim/*', 'test_run_data/*']},
author='Martin Hunt',
author_email='path-help@sanger.ac.uk',
url='https://github.com/sanger-pathogens/iva',
scripts=glob.glob('scripts/*'),
test_suite='nose.collector',
tests_require=['nose >= 1.3'],
install_requires=[
'pyfastaq >= 3.10.0',
'networkx >= 1.7',
'pysam >= 0.8.1',
'packaging'
],
license='GPLv3',
classifiers=[
'Development Status :: 4 - Beta',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Programming Language :: Python :: 3 :: Only',
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
],
)
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