+ changed PipelinHeuristic to support new data access functions
[qpalma.git] / standalone / setup.py
1 #!/usr/bin/env python2.4
2
3 import sys
4 #import os
5 import shutil
6 from distutils.core import setup, Extension
7
8 try:
9 import numpy
10 except:
11 sys.stderr.write("WARNING: did not find 'numpy'\n")
12
13 try:
14 import shogun
15 except:
16 sys.stderr.write("WARNING: did not find 'shogun'\n")
17 sys.stderr.write(" shogun is required for computing splice site scores\n")
18 sys.stderr.write(" See shogun website: http://www.shogun-toolbox.org)\n")
19
20 if sys.argv[1] != 'sdist':
21 sys.stderr.write('Using swig to construct interface file alignment_tool.py\n')
22 setup (name = 'palma._alignment_tool',
23 version = '0.3.7',
24 description = '!!!This is a hack to ensure that swig runs first. Real setup is below!!!',
25 author = ['Uta Schulze', 'Bettina Hepp', 'Gunnar Raetsch', \
26 'Soeren Sonnenburg','Cheng Soon Ong'],
27 author_email = ['Gunnar.Raetsch@tuebingen.mpg.de'],
28 license='GPL2',
29 url = 'http://www.fml.tuebingen.mpg.de/raetsch/projects/palma',
30 ext_modules = [Extension('palma._alignment_tool',
31 sources = ['src/bound_matrix.cpp', 'src/myalign_1best.cpp', \
32 'src/fill_matrix_1best.cpp', 'src/result_align_1best.cpp',\
33 'src/alignment_tool_1best.i'])],
34 options={'build_ext':{'swig_opts':'-c++'}},
35 )
36 shutil.copy2('src/alignment_tool.py','palma/alignment_tool.py')
37 #os.rename('src/alignment_tool.py','palma/alignment_tool.py')
38
39 sys.stderr.write('PALMA - mRNA to Genome Alignments using Large Margin Algorithms\n')
40 setup (name = 'palma',
41 version = '0.3.7',
42 description = 'PALMA - mRNA to Genome Alignments using Large Margin Algorithms',
43 author = ['Uta Schulze', 'Bettina Hepp', 'Gunnar Raetsch', \
44 'Soeren Sonnenburg','Cheng Soon Ong'],
45 author_email = ['Gunnar.Raetsch@tuebingen.mpg.de'],
46 license='GPL2',
47 url = 'http://www.fml.tuebingen.mpg.de/raetsch/projects/palma',
48 #py_modules=['palma.palma_utils','palma.alignment_tool','palma.genomic',\
49 py_modules=['palma.palma_utils','palma.genomic',\
50 'palma.model','palma.output_formating','palma.seqdict','palma.signal_detectors'],
51 ext_modules = [Extension('palma._alignment_tool',
52 sources = ['src/bound_matrix.cpp', 'src/myalign_1best.cpp', \
53 'src/fill_matrix_1best.cpp', 'src/result_align_1best.cpp',\
54 'src/alignment_tool_1best.i'])],
55 packages=['palma'],
56 package_data={'palma': ['data/*.param.bz2']},
57 scripts=['scripts/palma-align.py'],
58 options={'build_ext':{'swig_opts':'-c++'}},
59 long_description='''
60 PALMA aligns two genetic sequences 'the best way' according
61 to its underlying algorithm and trained parameters. See the paper on the website for details.''')
62
63 # cleanup swig outputs so that each build is clean
64 #os.remove('palma/alignment_tool.py')
65 #os.remove('src/alignment_tool_1best_wrap.cpp')