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annotate setup.py @ 5:c6b0f5c3f3b4 draft

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author bioitcore
date Wed, 13 Sep 2017 15:07:06 -0400
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1
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1 '''
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2 chimerascan
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3
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4 Created on Jan 5, 2011
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5
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6 @author: mkiyer
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7 '''
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8 from distutils.core import setup
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9 from distutils.extension import Extension
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10
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11 import os
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12 import glob
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13
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14 # local imports
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15 import chimerascan
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16
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17 # ------ Setup instructions -------------------------------------------------
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18
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19 setup_kwargs = {"name": "chimerascan",
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20 "version": chimerascan.__version__,
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21 "description": "chimeric transcript discovery from RNA-seq",
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22 "long_description": __doc__,
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23 "author": "Matthew Iyer",
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24 "author_email": "mkiyer@umich.edu",
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25 "license": "GPL3",
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26 "platforms": "Linux",
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27 "url": "http://chimerascan.googlecode.com",
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28 "packages": ["chimerascan",
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29 "chimerascan.pysam",
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30 "chimerascan.bx",
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31 "chimerascan.pipeline",
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32 "chimerascan.lib",
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33 "chimerascan.tools"],
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34 "package_data": {'chimerascan.tools': ['table_template.html']},
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35 "scripts": ["chimerascan/chimerascan_run.py",
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36 "chimerascan/chimerascan_index.py",
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37 "chimerascan/tools/chimerascan_html_table.py",
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38 "chimerascan/tools/gtf_to_genepred.py",
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39 "chimerascan/tools/make_false_positive_file.py"]}
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40
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41 # ---- Extension Modules ----------------------------------------------------
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42
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43 def get_cython_extension_modules():
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44 # pysam - samtools
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45 samtools = Extension("chimerascan.pysam.csamtools", # name of extension
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46 ["chimerascan/pysam/csamtools.pyx",
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47 "chimerascan/pysam/pysam_util.c"] +\
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48 glob.glob( os.path.join( "chimerascan", "pysam", "samtools", "*.c" )),
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49 library_dirs=[],
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50 include_dirs=[ "chimerascan/pysam/samtools", "chimerascan/pysam" ],
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51 libraries=[ "z", ],
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52 language="c",
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53 define_macros = [('FILE_OFFSET_BITS','64'),
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54 ('_USE_KNETFILE','')])
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55 # pysam - tabix
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56 tabix = Extension("chimerascan.pysam.ctabix", # name of extension
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57 ["chimerascan/pysam/ctabix.pyx" ] +\
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58 glob.glob(os.path.join("chimerascan", "pysam", "tabix", "*.c")),
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59 library_dirs=[],
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60 include_dirs=[ "chimerascan/pysam/tabix", "chimerascan/pysam" ],
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61 libraries=[ "z", ],
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62 language="c",
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63 )
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64 # Interval clustering
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65 bx_cluster = Extension("chimerascan.bx.cluster",
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66 ["chimerascan/bx/cluster.pyx", "chimerascan/bx/intervalcluster.c"],
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67 include_dirs=["chimerascan/bx"])
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68 # Interval intersection
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69 bx_interval = Extension("chimerascan.bx.intersection",
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70 ["chimerascan/bx/intersection.pyx" ])
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71 return [samtools, tabix, bx_cluster, bx_interval]
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72
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73 def get_c_extension_modules():
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74 # pysam - samtools
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75 samtools = Extension("chimerascan.pysam.csamtools", # name of extension
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76 ["chimerascan/pysam/csamtools.c",
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77 "chimerascan/pysam/pysam_util.c"] +\
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78 glob.glob( os.path.join( "chimerascan", "pysam", "samtools", "*.c" )),
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79 library_dirs=[],
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80 include_dirs=[ "chimerascan/pysam/samtools", "chimerascan/pysam" ],
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81 libraries=[ "z", ],
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82 language="c",
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83 define_macros = [('FILE_OFFSET_BITS','64'),
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84 ('_USE_KNETFILE','')])
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85 # pysam - tabix
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86 tabix = Extension("chimerascan.pysam.ctabix", # name of extension
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87 ["chimerascan/pysam/ctabix.c" ] +\
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88 glob.glob(os.path.join("chimerascan", "pysam", "tabix", "*.c")),
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89 library_dirs=[],
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90 include_dirs=[ "chimerascan/pysam/tabix", "chimerascan/pysam" ],
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91 libraries=[ "z", ],
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92 language="c",
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93 )
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94 # Interval clustering
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95 bx_cluster = Extension("chimerascan.bx.cluster",
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96 ["chimerascan/bx/cluster.c", "chimerascan/bx/intervalcluster.c"],
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97 include_dirs=["chimerascan/bx"])
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98 # Interval intersection
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99 bx_interval = Extension("chimerascan.bx.intersection",
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100 ["chimerascan/bx/intersection.c"])
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101 return [samtools, tabix, bx_cluster, bx_interval]
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102
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103 def main():
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104 setup(ext_modules=get_c_extension_modules(),
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105 **setup_kwargs)
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106
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107 if __name__ == '__main__':
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108 main()