#!/usr/bin/python

__author__      = "Sander Granneman"
__copyright__   = "Copyright 2020"
__version__     = "1.5.2"
__credits__     = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"]
__maintainer__  = ["Sander Granneman"]
__email__       = "sgrannem@staffmail.ed.ac.uk"
__status__      = "Production"


import re
import sys
import os

try:
	from setuptools import setup
	from setuptools.command import easy_install
	sys.stdout.write("Python development and setuptools have been installed...\n")
except:
	sys.stderr.write("Python development and setuptools have not been installed on this machine\nPlease contact the admin of this computer to install these modules\n")
	exit()

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','six >= 1.9.0'],
	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/scripts/pyGTF2Fasta.py'
				],
	classifiers=[   'Development Status :: 5 - Production/Stable',
					'Environment :: Console',
					'Intended Audience :: Education',
					'Intended Audience :: Developers',
					'Intended Audience :: Science/Research',
					'License :: Freeware',
					'Operating System :: MacOS :: MacOS X',
					'Operating System :: POSIX',
					'Programming Language :: Python :: 3.6',
					'Topic :: Scientific/Engineering :: Bio-Informatics',
					'Topic :: Software Development :: Libraries :: Application Frameworks'
				],
	data_files=[    ('pyCRAC/db/',[
					'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']),
					('pyCRAC/tests/',[
					'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']),
					('pyCRAC',[
					'The_pyCRAC_Manual.pdf'])
				]
			  )
