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- #!/usr/bin/python
- __author__ = "Sander Granneman"
- __copyright__ = "Copyright 2021"
- __version__ = "1.5.1"
- __credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"]
- __maintainer__ = ["Sander Granneman","Rob van Nues for SlackBuilds.org"]
- __email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"]
- __status__ = "Production"
- import sys
- import os
- import platform
- import setuptools
- from setuptools import setup
- from setuptools.command import easy_install
- DEFAULT_PATH = "/usr/share/"
- sys.stdout.write("\nInstalling pyCRAC version %s...\n" % __version__)
- 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/crac_pipelines/CRAC_pipeline_PE.py',
- 'pyCRAC/crac_pipelines/CRAC_pipeline_SE.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=[ ('%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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