1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
import glob
import sys
import os
from setuptools import setup, find_packages, Extension
from Cython.Distutils import build_ext
import pysam
test_module_suffix = os.path.dirname(os.path.abspath(__file__)).split(os.sep)[-1]
test_module_name = "PysamTestModule_{}".format(test_module_suffix)
pysam_libraries = pysam.get_libraries()
pysam_libdirs, pysam_libs = zip(*[os.path.split(x) for x in pysam_libraries])
pysam_libdir = pysam_libdirs[0]
# remove lib and .so
pysam_libs = [x[3:-3] for x in pysam_libs]
TestModule = Extension(
"{}.BuildRead".format(test_module_name),
["{}/BuildRead.pyx".format(test_module_name)],
include_dirs=pysam.get_include(),
library_dirs=[pysam_libdir],
libraries=pysam_libs,
language="C",
)
setup(
name=test_module_name,
version='0.1',
packages=find_packages(),
package_dir={test_module_name: test_module_name},
ext_modules=[TestModule],
cmdclass={'build_ext': build_ext},
)
|
