setup_slack.py 3.4 KB

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  1. #!/usr/bin/python
  2. __author__ = "Sander Granneman"
  3. __copyright__ = "Copyright 2021"
  4. __version__ = "1.5.1"
  5. __credits__ = ["Sander Granneman","Grzegorz Kudla","Hywell Dunn Davies"]
  6. __maintainer__ = ["Sander Granneman","Rob van Nues for SlackBuilds.org"]
  7. __email__ = ["sgrannem@staffmail.ed.ac.uk", "sborg63@disroot.org"]
  8. __status__ = "Production"
  9. import sys
  10. import os
  11. import platform
  12. import setuptools
  13. from setuptools import setup
  14. from setuptools.command import easy_install
  15. DEFAULT_PATH = "/usr/share/"
  16. sys.stdout.write("\nInstalling pyCRAC version %s...\n" % __version__)
  17. setup(name='pyCRAC',
  18. version='%s' % __version__,
  19. description='Python NextGen sequencing data processing software',
  20. author='Sander Granneman',
  21. author_email='sgrannem@staffmail.ed.ac.uk',
  22. url='http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html',
  23. packages=['pyCRAC','pyCRAC.Parsers','pyCRAC.Classes','pyCRAC.Methods'],
  24. install_requires=['numpy >= 1.5.1', 'cython >=0.19', 'pysam >= 0.6','six >= 1.9.0'],
  25. scripts=[
  26. 'pyCRAC/pyReadAligner.py',
  27. 'pyCRAC/pyMotif.py',
  28. 'pyCRAC/pyPileup.py',
  29. 'pyCRAC/pyBarcodeFilter.py',
  30. 'pyCRAC/pyReadCounters.py',
  31. 'pyCRAC/pyBinCollector.py',
  32. 'pyCRAC/pyCalculateFDRs.py',
  33. 'pyCRAC/pyClusterReads.py',
  34. 'pyCRAC/pyCalculateMutationFrequencies.py',
  35. 'pyCRAC/scripts/pyCalculateChromosomeLengths.py',
  36. 'pyCRAC/scripts/pyFastqDuplicateRemover.py',
  37. 'pyCRAC/scripts/pyAlignment2Tab.py',
  38. 'pyCRAC/scripts/pyGetGTFSources.py',
  39. 'pyCRAC/scripts/pySelectMotifsFromGTF.py',
  40. 'pyCRAC/scripts/pyFasta2tab.py',
  41. 'pyCRAC/scripts/pyFastqJoiner.py',
  42. 'pyCRAC/scripts/pyFastqSplitter.py',
  43. 'pyCRAC/scripts/pyExtractLinesFromGTF.py',
  44. 'pyCRAC/scripts/pyGetGeneNamesFromGTF.py',
  45. 'pyCRAC/scripts/pyCheckGTFfile.py',
  46. 'pyCRAC/scripts/pybed2GTF.py',
  47. 'pyCRAC/scripts/pyGTF2sgr.py',
  48. 'pyCRAC/scripts/pyGTF2bed.py',
  49. 'pyCRAC/scripts/pyGTF2bedGraph.py',
  50. 'pyCRAC/scripts/pyFilterGTF.py',
  51. 'pyCRAC/scripts/pyNormalizeIntervalLengths.py',
  52. 'pyCRAC/crac_pipelines/CRAC_pipeline_PE.py',
  53. 'pyCRAC/crac_pipelines/CRAC_pipeline_SE.py',
  54. ],
  55. classifiers=[ 'Development Status :: 5 - Production/Stable',
  56. 'Environment :: Console',
  57. 'Intended Audience :: Education',
  58. 'Intended Audience :: Developers',
  59. 'Intended Audience :: Science/Research',
  60. 'License :: Freeware',
  61. 'Operating System :: MacOS :: MacOS X',
  62. 'Operating System :: POSIX',
  63. 'Programming Language :: Python :: 3.6',
  64. 'Topic :: Scientific/Engineering :: Bio-Informatics',
  65. 'Topic :: Software Development :: Libraries :: Application Frameworks'
  66. ],
  67. data_files=[ ('%spyCRAC-%s/db/' % (DEFAULT_PATH,__version__), [
  68. 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt',
  69. 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf',
  70. 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa',
  71. 'pyCRAC/db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab']),
  72. ('%spyCRAC-%s/tests/' % (DEFAULT_PATH,__version__), [
  73. 'tests/test.novo',
  74. 'tests/test.sh',
  75. 'tests/test_coordinates.txt',
  76. 'tests/test.gtf',
  77. 'tests/test_f.fastq',
  78. 'tests/test_f.fastq.gz',
  79. 'tests/test_f_dm.fastq',
  80. 'tests/test_r.fastq',
  81. 'tests/test_r.fastq.gz',
  82. 'tests/test_r_dm.fastq',
  83. 'tests/indexes.txt',
  84. 'tests/barcodes.txt',
  85. 'tests/genes.list'])
  86. ]
  87. )