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104 lines
4 KiB
Python
104 lines
4 KiB
Python
#!/usr/bin/python
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# not compatible with python 3
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__author__ = "Sander Granneman"
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__copyright__ = "Copyright 2017"
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__version__ = "1.2.4.0"
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__credits__ = ["Sander Granneman","Hywell Dunn Davies"]
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__maintainer__ = ["Rob van Nues, via SlackBuilds.org"]
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__email__ = "sgrannem@staffmail.ed.ac.uk"
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__status__ = "Production"
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import sys
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import os
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import platform
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import setuptools
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from setuptools import setup
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DEFAULT_PATH = "/usr/share/"
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if sys.version[0:3] < '2.7' : raise ImportError('Python version 2.7 or above is required for pyCRAC')
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if sys.version[0:3] >= '3.0': raise ImportError('pyCRAC is not compatible with Python 3.0 or higher')
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sys.stdout.write("\nInstalling pyCRAC version %s...\n" % __version__)
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path_files = open("pyCRAC/defaults.py","w")
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#path_files.write("DEFAULT_PATH=\"%s\"\n" % DEFAULT_PATH)
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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__))
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path_files.close()
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setup(name='pyCRAC',
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version='%s' % __version__,
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description='Python NextGen sequencing data processing software',
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author='Sander Granneman',
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author_email='sgrannem@staffmail.ed.ac.uk',
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url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html',
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packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'],
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install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6'],
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scripts=[
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'pyCRAC/pyReadAligner.py',
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'pyCRAC/pyMotif.py',
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'pyCRAC/pyPileup.py',
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'pyCRAC/pyBarcodeFilter.py',
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'pyCRAC/pyReadCounters.py',
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'pyCRAC/pyBinCollector.py',
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'pyCRAC/pyCalculateFDRs.py',
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'pyCRAC/pyClusterReads.py',
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'pyCRAC/pyCalculateMutationFrequencies.py',
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'pyCRAC/scripts/pyCalculateChromosomeLengths.py',
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'pyCRAC/scripts/pyFastqDuplicateRemover.py',
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'pyCRAC/scripts/pyAlignment2Tab.py',
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'pyCRAC/scripts/pyGetGTFSources.py',
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'pyCRAC/scripts/pySelectMotifsFromGTF.py',
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'pyCRAC/scripts/pyFasta2tab.py',
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'pyCRAC/scripts/pyFastqJoiner.py',
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'pyCRAC/scripts/pyFastqSplitter.py',
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'pyCRAC/scripts/pyExtractLinesFromGTF.py',
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'pyCRAC/scripts/pyGetGeneNamesFromGTF.py',
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'pyCRAC/scripts/pyCheckGTFfile.py',
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'pyCRAC/scripts/pybed2GTF.py',
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'pyCRAC/scripts/pyGTF2sgr.py',
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'pyCRAC/scripts/pyGTF2bed.py',
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'pyCRAC/scripts/pyGTF2bedGraph.py',
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'pyCRAC/scripts/pyFilterGTF.py',
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'pyCRAC/scripts/pyNormalizeIntervalLengths.py',
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'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PE.py',
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'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_PeakFinder.py',
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'pyCRAC/kinetic_crac_pipeline/CRAC_pipeline_SE.py',
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'pyCRAC/kinetic_crac_pipeline/TrimNucs.py'
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],
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classifiers=[ 'Development Status :: 5 - Production/Stable',
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'Environment :: Terminal',
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'Intended Audience :: Education',
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'Intended Audience :: Developers',
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'Intended Audience :: Science/Research',
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'License :: Freeware',
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'Operating System :: MacOS :: MacOS X',
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'Operating System :: POSIX',
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'Programming Language :: Python :: 2.7',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Software Development :: Libraries :: Application Frameworks'
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],
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data_files=[ ('%spyCRAC-%s/db/' % (DEFAULT_PATH,__version__), [
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'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt',
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'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf',
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'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa',
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'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab']),
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('%spyCRAC-%s/tests/' % (DEFAULT_PATH,__version__), [
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'tests/test.novo',
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'tests/test.sh',
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'tests/test_coordinates.txt',
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'tests/test.gtf',
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'tests/test_f.fastq',
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'tests/test_f.fastq.gz',
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'tests/test_f_dm.fastq',
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'tests/test_r.fastq',
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'tests/test_r.fastq.gz',
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'tests/test_r_dm.fastq',
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'tests/indexes.txt',
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'tests/barcodes.txt',
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'tests/genes.list'])
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]
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)
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