#!/usr/bin/python # not compatible with python 3 __author__ = "Sander Granneman" __copyright__ = "Copyright 2017" __version__ = "1.2.4.0" __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']) ] )