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comparison setup.py @ 1:b9877fa1159a draft

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planemo upload commit 93e677982c3636da455de2f827a87e516c7985ac-dirty
author bioitcore
date Tue, 12 Sep 2017 13:57:02 -0400
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0:d85dea371064 1:b9877fa1159a
1 '''
2 chimerascan
3
4 Created on Jan 5, 2011
5
6 @author: mkiyer
7 '''
8 from distutils.core import setup
9 from distutils.extension import Extension
10
11 import os
12 import glob
13
14 # local imports
15 import chimerascan
16
17 # ------ Setup instructions -------------------------------------------------
18
19 setup_kwargs = {"name": "chimerascan",
20 "version": chimerascan.__version__,
21 "description": "chimeric transcript discovery from RNA-seq",
22 "long_description": __doc__,
23 "author": "Matthew Iyer",
24 "author_email": "mkiyer@umich.edu",
25 "license": "GPL3",
26 "platforms": "Linux",
27 "url": "http://chimerascan.googlecode.com",
28 "packages": ["chimerascan",
29 "chimerascan.pysam",
30 "chimerascan.bx",
31 "chimerascan.pipeline",
32 "chimerascan.lib",
33 "chimerascan.tools"],
34 "package_data": {'chimerascan.tools': ['table_template.html']},
35 "scripts": ["chimerascan/chimerascan_run.py",
36 "chimerascan/chimerascan_index.py",
37 "chimerascan/tools/chimerascan_html_table.py",
38 "chimerascan/tools/gtf_to_genepred.py",
39 "chimerascan/tools/make_false_positive_file.py"]}
40
41 # ---- Extension Modules ----------------------------------------------------
42
43 def get_cython_extension_modules():
44 # pysam - samtools
45 samtools = Extension("chimerascan.pysam.csamtools", # name of extension
46 ["chimerascan/pysam/csamtools.pyx",
47 "chimerascan/pysam/pysam_util.c"] +\
48 glob.glob( os.path.join( "chimerascan", "pysam", "samtools", "*.c" )),
49 library_dirs=[],
50 include_dirs=[ "chimerascan/pysam/samtools", "chimerascan/pysam" ],
51 libraries=[ "z", ],
52 language="c",
53 define_macros = [('FILE_OFFSET_BITS','64'),
54 ('_USE_KNETFILE','')])
55 # pysam - tabix
56 tabix = Extension("chimerascan.pysam.ctabix", # name of extension
57 ["chimerascan/pysam/ctabix.pyx" ] +\
58 glob.glob(os.path.join("chimerascan", "pysam", "tabix", "*.c")),
59 library_dirs=[],
60 include_dirs=[ "chimerascan/pysam/tabix", "chimerascan/pysam" ],
61 libraries=[ "z", ],
62 language="c",
63 )
64 # Interval clustering
65 bx_cluster = Extension("chimerascan.bx.cluster",
66 ["chimerascan/bx/cluster.pyx", "chimerascan/bx/intervalcluster.c"],
67 include_dirs=["chimerascan/bx"])
68 # Interval intersection
69 bx_interval = Extension("chimerascan.bx.intersection",
70 ["chimerascan/bx/intersection.pyx" ])
71 return [samtools, tabix, bx_cluster, bx_interval]
72
73 def get_c_extension_modules():
74 # pysam - samtools
75 samtools = Extension("chimerascan.pysam.csamtools", # name of extension
76 ["chimerascan/pysam/csamtools.c",
77 "chimerascan/pysam/pysam_util.c"] +\
78 glob.glob( os.path.join( "chimerascan", "pysam", "samtools", "*.c" )),
79 library_dirs=[],
80 include_dirs=[ "chimerascan/pysam/samtools", "chimerascan/pysam" ],
81 libraries=[ "z", ],
82 language="c",
83 define_macros = [('FILE_OFFSET_BITS','64'),
84 ('_USE_KNETFILE','')])
85 # pysam - tabix
86 tabix = Extension("chimerascan.pysam.ctabix", # name of extension
87 ["chimerascan/pysam/ctabix.c" ] +\
88 glob.glob(os.path.join("chimerascan", "pysam", "tabix", "*.c")),
89 library_dirs=[],
90 include_dirs=[ "chimerascan/pysam/tabix", "chimerascan/pysam" ],
91 libraries=[ "z", ],
92 language="c",
93 )
94 # Interval clustering
95 bx_cluster = Extension("chimerascan.bx.cluster",
96 ["chimerascan/bx/cluster.c", "chimerascan/bx/intervalcluster.c"],
97 include_dirs=["chimerascan/bx"])
98 # Interval intersection
99 bx_interval = Extension("chimerascan.bx.intersection",
100 ["chimerascan/bx/intersection.c"])
101 return [samtools, tabix, bx_cluster, bx_interval]
102
103 def main():
104 setup(ext_modules=get_c_extension_modules(),
105 **setup_kwargs)
106
107 if __name__ == '__main__':
108 main()