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#!/usr/bin/python
# not compatible with python 3
__author__ = "Sander Granneman"
__copyright__ = "Copyright 2018"
__version__ = "1.3.3"
__credits__ = ["Sander Granneman","Hywell Dunn Davies"]
__maintainer__ = ["Rob van Nues, via SlackBuilds.org"]
__email__ = "sgrannem@staffmail.ed.ac.uk"
__status__ = "Production"
import sys
import os
import platform
import setuptools
from setuptools import setup
DEFAULT_PATH = "/usr/share/"
if sys.version[0:3] < '2.7' : raise ImportError('Python version 2.7 or above is required for pyCRAC')
if sys.version[0:3] >= '3.0': raise ImportError('pyCRAC is not compatible with Python 3.0 or higher')
sys.stdout.write("\nInstalling pyCRAC version %s...\n" % __version__)
path_files = open("pyCRAC/defaults.py","w")
#path_files.write("DEFAULT_PATH=\"%s\"\n" % DEFAULT_PATH)
path_files.write("GTF=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf\"\nTAB=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab\"\nCHROM=\"%spyCRAC-%s/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt\"\n" % (DEFAULT_PATH,__version__,DEFAULT_PATH,__version__,DEFAULT_PATH,__version__))
path_files.close()
setup(name='pyCRAC',
version='%s' % __version__,
description='Python NextGen sequencing data processing software',
author='Sander Granneman',
author_email='sgrannem@staffmail.ed.ac.uk',
url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html',
packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'],
install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6'],
scripts=[
'pyCRAC/pyReadAligner.py',
'pyCRAC/pyMotif.py',
'pyCRAC/pyPileup.py',
'pyCRAC/pyBarcodeFilter.py',
'pyCRAC/pyReadCounters.py',
'pyCRAC/pyBinCollector.py',
'pyCRAC/pyCalculateFDRs.py',
'pyCRAC/pyClusterReads.py',
'pyCRAC/pyCalculateMutationFrequencies.py',
'pyCRAC/scripts/pyCalculateChromosomeLengths.py',
'pyCRAC/scripts/pyFastqDuplicateRemover.py',
'pyCRAC/scripts/pyAlignment2Tab.py',
'pyCRAC/scripts/pyGetGTFSources.py',
'pyCRAC/scripts/pySelectMotifsFromGTF.py',
'pyCRAC/scripts/pyFasta2tab.py',
'pyCRAC/scripts/pyFastqJoiner.py',
'pyCRAC/scripts/pyFastqSplitter.py',
'pyCRAC/scripts/pyExtractLinesFromGTF.py',
'pyCRAC/scripts/pyGetGeneNamesFromGTF.py',
'pyCRAC/scripts/pyCheckGTFfile.py',
'pyCRAC/scripts/pybed2GTF.py',
'pyCRAC/scripts/pyGTF2sgr.py',
'pyCRAC/scripts/pyGTF2bed.py',
'pyCRAC/scripts/pyGTF2bedGraph.py',
'pyCRAC/scripts/pyFilterGTF.py',
'pyCRAC/scripts/pyNormalizeIntervalLengths.py',
'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py',
'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py',
'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py',
'pyCRAC/kinetic_crac_pipeline/TrimNucs.py'
],
classifiers=[ 'Development Status :: 5 - Production/Stable',
'Environment :: Terminal',
'Intended Audience :: Education',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: Freeware',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Programming Language :: Python :: 2.7',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Software Development :: Libraries :: Application Frameworks'
],
data_files=[ ('%spyCRAC-%s/db/' % (DEFAULT_PATH,__version__), [
'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt',
'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf',
'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa',
'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab']),
('%spyCRAC-%s/tests/' % (DEFAULT_PATH,__version__), [
'tests/test.novo',
'tests/test.sh',
'tests/test_coordinates.txt',
'tests/test.gtf',
'tests/test_f.fastq',
'tests/test_f.fastq.gz',
'tests/test_f_dm.fastq',
'tests/test_r.fastq',
'tests/test_r.fastq.gz',
'tests/test_r_dm.fastq',
'tests/indexes.txt',
'tests/barcodes.txt',
'tests/genes.list'])
]
)
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