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setup.py
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setup.py
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"""Description
Setup script to install genomics/bcftbx
Copyright (C) University of Manchester 2011-15 Peter Briggs
"""
# Hack to acquire all scripts that we want to
# install into 'bin'
from glob import glob
scripts = []
for pattern in ('build-indexes/*.sh',
'ChIP-seq/*.pl','ChIP-seq/*.py',
'illumina2cluster/*.py','illumina2cluster/*.sh',
'microarray/*.py',
'NGS-general/*.pl','NGS-general/*.py','NGS-general/*.sh',
'QC-pipeline/*.py','QC-pipeline/*.sh',
'RNA-seq/*.py',
'solid2cluster/*.py','solid2cluster/*.sh',
'utils/*.pl','utils/*.py','utils/*.R','utils/*.sh'):
scripts.extend(glob(pattern))
# Setup for installation etc
from setuptools import setup
import bcftbx
setup(name = "genomics-bcftbx",
version = bcftbx.__version__,
description = 'Utilities for NGS and genomic bioinformatics',
long_description = """Utility programs and libraries used for Next Generation
Sequencing (NGS) and genomic bioinformatics, developed and used within the
Bioinformatics Core Facility (BCF) at the University of Manchester""",
url = 'https://github.com/fls-bioinformatics-core/genomics',
maintainer = 'Peter Briggs',
maintainer_email = 'peter.briggs@manchester.ac.uk',
packages = ['bcftbx','bcftbx.qc'],
license = 'Artistic License',
# Pull in dependencies
install_requires = ['xlwt >= 0.7.2',
'xlrd >= 0.7.1',
'xlutils >= 1.4.1',
'xlsxwriter >= 0.8.4',],
# Enable 'python setup.py test'
test_suite='nose.collector',
tests_require=['nose'],
# Scripts
scripts = scripts,
# Configuration file for QC
data_files = [('config',['config/qc.setup.sample']),
('share',['share/bcftbx.functions.sh',
'share/bcftbx.ngs_utils.sh',
'share/bcftbx.versions.sh',
'share/bcftbx.lock.sh']),
('bin/qc_boxplotter',
['QC-pipeline/qc_boxplotter/colour_QC_script.sh',
'QC-pipeline/qc_boxplotter/qual2Rinput_file_per_posn.pl',
'QC-pipeline/qc_boxplotter/SOLiD_qual_boxplot.R'])],
include_package_data=True,
zip_safe = False)